4YBH | pdb_00004ybh

Crystal structure of the human RAGE ectodomain (VC1C2 fragment) in complex with human S100A6

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4ybhb_	All alpha proteins	EF Hand-like	EF-hand	S100 proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	EF-hand	8040106	3001983	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	LRR_1+LRR_8+LRR_14	e4ybhB1	A: a/b three-layered sandwiches	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F: LRR_1+LRR_8+LRR_14	ECOD (v294.1)
A	LRR_1+LRR_8+LRR_14	e4ybhA1	A: a/b three-layered sandwiches	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F: LRR_1+LRR_8+LRR_14	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A	AGER (Advanced glycosylation end product-specific receptor)	1V-1C-1C-LIKE	Homo sapiens (human)	AGER*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	(1V-1C-1C-LIKE)	IMGT (202611-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01023	S-100/ICaBP type calcium binding domain (S_100)	S-100/ICaBP type calcium binding domain	The S-100 domain is a subfamily of the EF-hand calcium binding proteins.	Domain
A	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
A	PF08205	CD80-like C2-set immunoglobulin domain (C2-set_2)	CD80-like C2-set immunoglobulin domain	These domains belong to the immunoglobulin superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Protein S100-A6	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding S100 protein binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding tropomyosin binding monoatomic ion transmembrane transporter activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding S100 protein binding identical protein binding protein homodimerization activity protein dimerization activity cytoskeletal protein binding tropomyosin binding monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity calcium-dependent protein binding transition metal ion binding zinc ion binding	regulation of biological process fibroblast proliferation cell population proliferation regulation of cellular process positive regulation of cell population proliferation biological regulation positive regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation cellular process positive regulation of cellular process cellular response to stimulus response to stimulus regulation of biological process fibroblast proliferation cell population proliferation regulation of cellular process positive regulation of cell population proliferation biological regulation positive regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation cellular process positive regulation of cellular process cellular response to stimulus response to stimulus signaling signal transduction cell communication multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane membrane extracellular matrix external encapsulating structure ruffle cell projection cell leading edge plasma membrane bounded cell projection perinuclear region of cytoplasm cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane
A	Advanced glycosylation end product-specific receptor	protein binding binding histone binding amyloid-beta binding peptide binding cargo receptor activity scavenger receptor activity cell adhesion molecule binding laminin receptor activity cell adhesion mediator activity DNA binding nucleic acid binding molecular transducer activity signaling receptor activity protein binding binding histone binding amyloid-beta binding peptide binding cargo receptor activity scavenger receptor activity cell adhesion molecule binding laminin receptor activity cell adhesion mediator activity DNA binding nucleic acid binding molecular transducer activity signaling receptor activity advanced glycation end-product receptor activity protein-containing complex binding molecular adaptor activity identical protein binding transmembrane signaling receptor activity RNA binding S100 protein binding	negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling amyloid precursor protein catabolic process positive regulation of protein metabolic process regulation of protein metabolic process primary metabolic process regulation of amyloid precursor protein catabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process positive regulation of amyloid precursor protein catabolic process amyloid precursor protein metabolic process regulation of metabolic process positive regulation of locomotion regulation of cell motility positive regulation of monocyte extravasation positive regulation of cell migration monocyte extravasation positive regulation of cell motility cellular extravasation myeloid leukocyte migration regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration positive regulation of immune system process locomotion regulation of leukocyte migration positive regulation of leukocyte migration leukocyte migration immune system process regulation of locomotion mononuclear cell migration regulation of monocyte extravasation regulation of cellular extravasation positive regulation of cellular extravasation localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport regulation of leukocyte differentiation multicellular organismal process cellular developmental process regulation of developmental process cell development mononuclear cell differentiation regulation of cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of hemopoiesis positive regulation of cell differentiation cell differentiation anatomical structure development regulation of multicellular organismal process developmental process regulation of multicellular organismal development hemopoiesis positive regulation of cell development regulation of dendritic cell differentiation regulation of hemopoiesis positive regulation of multicellular organismal process dendritic cell differentiation positive regulation of leukocyte differentiation positive regulation of dendritic cell differentiation leukocyte differentiation interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of biosynthetic process regulation of interleukin-1 production gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process interleukin-1 beta production positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of cytokine production adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains leukocyte mediated immunity regulation of T cell mediated immunity T cell mediated cytotoxicity immune response regulation of adaptive immune response regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity adaptive immune response immune effector process regulation of T cell mediated cytotoxicity regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of response to stimulus regulation of immune response regulation of cell killing cell killing cellular response to stimulus positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of chemokine production chemokine production positive regulation of chemokine production astrocyte differentiation astrocyte activation glial cell development neurogenesis astrocyte development gliogenesis response to stress system development defense response cell activation nervous system development central nervous system development glial cell differentiation glial cell activation inflammatory response neuroinflammatory response DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response DNA repair response to wounding negative regulation of connective tissue replacement involved in inflammatory response wound healing wound healing negative regulation of tissue remodeling connective tissue replacement involved in inflammatory response wound healing wound healing involved in inflammatory response negative regulation of connective tissue replacement regulation of tissue remodeling inflammatory response to wounding tissue remodeling connective tissue replacement regulation of connective tissue replacement negative regulation of multicellular organismal process cellular localization macromolecule localization intracellular protein localization localization within membrane protein localization to membrane response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion heterotypic cell-cell adhesion cell adhesion cell-cell adhesion positive regulation of heterotypic cell-cell adhesion regulation of cell-cell adhesion regulation of heterotypic cell-cell adhesion system process circulatory system process vascular process in circulatory system vascular transport transport across blood-brain barrier regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation regulation of T cell activation lymphocyte activation leukocyte activation regulation of CD4-positive, alpha-beta T cell activation T cell activation CD4-positive, alpha-beta T cell activation alpha-beta T cell activation regulation of lymphocyte activation myeloid leukocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation plasma membrane bounded cell projection organization cell projection organization neuron projection development cellular component organization generation of neurons neuron differentiation neuron development cellular component organization or biogenesis regulation of endothelin production positive regulation of endothelin production endothelin production hexose mediated signaling homeostatic process response to monosaccharide response to carbohydrate carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose sugar mediated signaling pathway glucose mediated signaling pathway cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis chemical homeostasis response to glucose response to chemical glucose homeostasis carbohydrate mediated signaling regulation of double-strand break repair regulation of cellular response to stress positive regulation of DNA repair regulation of response to stress regulation of nucleobase-containing compound metabolic process double-strand break repair positive regulation of double-strand break repair regulation of DNA repair positive regulation of DNA metabolic process regulation of DNA metabolic process DNA replication positive chemotaxis chemotaxis regulation of response to external stimulus positive regulation of positive chemotaxis response to external stimulus induction of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis regulation of positive chemotaxis positive regulation of response to external stimulus taxis positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production spontaneous synaptic transmission regulation of spontaneous synaptic transmission positive regulation of DNA replication DNA-templated DNA replication positive regulation of DNA-templated DNA replication regulation of DNA-templated DNA replication regulation of DNA replication regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production regulation of monocyte chemotactic protein-1 production positive regulation of monocyte chemotactic protein-1 production monocyte chemotactic protein-1 production negative regulation of interleukin-10 production interleukin-10 production negative regulation of cellular process regulation of interleukin-10 production negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process non-canonical NF-kappaB signal transduction regulation of non-canonical NF-kappaB signal transduction response to nitrogen compound response to amyloid-beta positive regulation of cell population proliferation positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of activated T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation regulation of activated T cell proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion activated T cell proliferation positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation cell surface receptor signaling pathway regulation of defense response regulation of inflammatory response p38MAPK cascade regulation of p38MAPK cascade transcytosis regulation of system process negative regulation of blood circulation regulation of blood circulation blood circulation behavior learning or memory nervous system process cognition negative regulation of signaling negative regulation of synaptic transmission negative regulation of cell communication negative regulation of long-term synaptic depression long-term synaptic depression regulation of long-term synaptic depression positive regulation of non-canonical NF-kappaB signal transduction positive regulation of p38MAPK cascade regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production cellular response to nitrogen compound cellular response to amyloid-beta	phagocytic cup cell periphery cellular anatomical structure plasma membrane membrane postsynapse synapse cell junction apical part of cell plasma membrane region apical plasma membrane cell surface membrane-bounded organelle intracellular anatomical structure phagocytic cup cell periphery cellular anatomical structure plasma membrane membrane postsynapse synapse cell junction apical part of cell plasma membrane region apical plasma membrane cell surface membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle extracellular region nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center membraneless organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001751	S100/Calcium binding protein 7/8-like, conserved site	Conserved Site
B	IPR002048	EF-hand domain	Domain
B	IPR011992	EF-hand domain pair	Homologous Superfamily
B	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
B	IPR013787	S100/CaBP-9k-type, calcium binding, subdomain	Domain
B	IPR034118	Protein S100-A6	Family
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR003598	Immunoglobulin subtype 2	Domain
A	IPR051116	Cell Surface Receptors and Adhesion Molecules	Family
A	IPR013162	CD80-like, immunoglobulin C2-set	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P06703	medulloblastoma Liver Cirrhosis, Experimental sarcomatoid carcinoma intracranial vasospasm adult medulloblastoma medullomyoblastoma with myogenic differentiation carcinoma childhood medulloblastoma type 2 diabetes mellitus melanotic medulloblastoma juvenile dermatomyositis malignant glioma mammary neoplasms, animal adrenal cortex carcinoma osteosarcoma medulloblastoma Liver Cirrhosis, Experimental sarcomatoid carcinoma intracranial vasospasm adult medulloblastoma medullomyoblastoma with myogenic differentiation carcinoma childhood medulloblastoma type 2 diabetes mellitus melanotic medulloblastoma juvenile dermatomyositis malignant glioma mammary neoplasms, animal adrenal cortex carcinoma osteosarcoma breast cancer pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma Emery-Dreifuss muscular dystrophy transitional cell carcinoma large cell medulloblastoma lung cancer malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pituitary cancer gastric carcinoma invasive ductal breast carcinoma limb-girdle muscular dystrophy malignant ependymoma maturity-onset diabetes of the young Becker muscular dystrophy pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia desmoplastic/nodular medulloblastoma psoriasis Duchenne muscular dystrophy subependymal giant cell astrocytoma glioblastoma undifferentiated carcinoma
A	Pharos: Q15109	rheumatoid arthritis hyperglycemia neuralgia Inflammation atherosclerosis Lewy body dementia lung carcinoma diabetic peripheral angiopathy prostate carcinoma inborn carbohydrate metabolic disorder squamous cell lung carcinoma lung adenocarcinoma malignant glioma age-related macular degeneration membranous glomerulonephritis rheumatoid arthritis hyperglycemia neuralgia Inflammation atherosclerosis Lewy body dementia lung carcinoma diabetic peripheral angiopathy prostate carcinoma inborn carbohydrate metabolic disorder squamous cell lung carcinoma lung adenocarcinoma malignant glioma age-related macular degeneration membranous glomerulonephritis autism spectrum disorder chronic obstructive pulmonary disease osteoarthritis osteosarcoma hepatitis B virus infection psoriasis sarcoidosis systemic lupus erythematosus lung cancer ulcerative colitis malignant mesothelioma colorectal cancer osteoarthritis susceptibility 1 glioblastoma pancreas disease psoriatic arthritis schizophrenia systemic sclerosis wet macular degeneration arteriosclerosis disorder atopic eczema cervical cancer non-small cell lung carcinoma heart disease

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.