4D1M | pdb_00004d1m

Tetramerization domain of zebrafish p53 (crystal form II)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d4d1ml_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
K	d4d1mk_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
J	d4d1mj_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
I	d4d1mi_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
H	d4d1mh_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
G	d4d1mg_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
F	d4d1mf_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
E	d4d1me_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
D	d4d1md_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
C	d4d1mc_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
B	d4d1mb_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
A	d4d1ma_	All alpha proteins	p53 tetramerization domain	p53 tetramerization domain	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	p53 tetramerization domain	8072263	3000414	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)
L		e4d1mL1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
K		e4d1mK1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
J		e4d1mJ1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
I		e4d1mI1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
H		e4d1mH1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
G		e4d1mG1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
F		e4d1mF1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
E		e4d1mE1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
D		e4d1mD1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
C		e4d1mC1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
B		e4d1mB1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)
A		e4d1mA1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: HicA_toxin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)
H	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)
G	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)
F	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)
E	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)
C	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)
B	4.10.170.10	Few Secondary Structures	Irregular	p53, subunit A	p53-like tetramerisation domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF07710	P53 tetramerisation motif (P53_tetramer)	P53 tetramerisation motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	CELLULAR TUMOR ANTIGEN P53	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding transcription regulator activity DNA-binding transcription factor activity	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation tissue morphogenesis anatomical structure morphogenesis epithelium development epidermis morphogenesis epidermis development anatomical structure development developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation tissue morphogenesis anatomical structure morphogenesis epithelium development epidermis morphogenesis epidermis development anatomical structure development morphogenesis of an epithelium tissue development multicellular organismal process erythrocyte development cellular developmental process homeostatic process hemopoiesis cell development erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process cell differentiation myeloid cell development homeostasis of number of cells cellular process myeloid cell homeostasis erythrocyte homeostasis response to stimulus response to chemical response to methylmercury cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus catabolic process autophagy metabolic process process utilizing autophagic mechanism response to X-ray response to ionizing radiation response to radiation apoptotic process cell death programmed cell death regulation of biological process regulation of cellular process negative regulation of cellular process biological regulation negative regulation of biological process negative regulation of cell cycle cell cycle regulation of cell cycle positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process neuron apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process cellular senescence regulation of protein stability regulation of biological quality response to light stimulus response to UV hematopoietic stem cell homeostasis system process epithelial structure maintenance digestive system process intestinal epithelial structure maintenance tissue homeostasis maintenance of gastrointestinal epithelium digestion anatomical structure homeostasis definitive hemopoiesis negative regulation of cell division cell division regulation of cell division DNA damage checkpoint signaling regulation of cell cycle phase transition signaling cell cycle phase transition intracellular signal transduction cell communication negative regulation of cell cycle phase transition signal transduction cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway cellular response to transforming growth factor beta stimulus response to endogenous stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of cell cycle negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process negative regulation of metabolic process regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process apoptotic signaling pathway intrinsic apoptotic signaling pathway regulation of signal transduction regulation of intrinsic apoptotic signaling pathway regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator regulation of signaling signal transduction by p53 class mediator regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway regulation of double-strand break repair regulation of cellular response to stress regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of response to stress regulation of nucleobase-containing compound metabolic process DNA repair double-strand break repair primary metabolic process DNA metabolic process nucleic acid metabolic process regulation of DNA repair regulation of DNA metabolic process regulation of developmental process regulation of oogenesis regulation of reproductive process cellular process involved in reproduction in multicellular organism regulation of cell differentiation female gamete generation regulation of cell development regulation of multicellular organismal process oogenesis germ cell development positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cell population proliferation regulation of cell population proliferation apoptotic process involved in morphogenesis blood vessel morphogenesis tube development vasculature development circulatory system development apoptotic process involved in development multicellular organism development tube morphogenesis apoptotic process involved in blood vessel morphogenesis blood vessel development system development DNA damage response, signal transduction by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage transcription by RNA polymerase II regulation of transcription by RNA polymerase II angiogenesis regulation of vasculature development regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis negative regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process erythrocyte maturation developmental maturation anatomical structure maturation cell maturation	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR012346	p53/RUNT-type transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036674	p53-like tetramerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011615	p53, DNA-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR057064	p53, central conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002117	p53 tumour suppressor family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR010991	p53, tetramerisation domain	Domain

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.