4RH7 | pdb_00004rh7

Crystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	AAA_9_C	e4rh7A11	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_9_C	ECOD (1.6)
A	AAA_7_C	e4rh7A7	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_7_C	ECOD (1.6)
A	KOG3595	e4rh7A15	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG3595	ECOD (1.6)
A	AAA_6_C	e4rh7A3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_6_C	ECOD (1.6)
A	Dynein_heavy_2nd	e4rh7A13	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Dynein_heavy_2nd	ECOD (1.6)
A	EUF07951	e4rh7A5	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: EUF07951	ECOD (1.6)
A	MT	e4rh7A9	A: alpha bundles	X: Microtubule-Binding Domain of Flagellar Dynein (From Topology)	H: Microtubule-Binding Domain of Flagellar Dynein (From Topology)	T: Microtubule-Binding Domain of Flagellar Dynein	F: MT	ECOD (1.6)
A	DHC_N2	e4rh7A1	A: alpha superhelices	X: Linker domain of cytoplasmic dynein heavy chain (From Topology)	H: Linker domain of cytoplasmic dynein heavy chain (From Topology)	T: Linker domain of cytoplasmic dynein heavy chain	F: DHC_N2	ECOD (1.6)
A	Dynein_heavy_3rd	e4rh7A14	A: a+b complex topology	X: C-terminal domain of cytoplasmic dynein heavy chain (From Topology)	H: C-terminal domain of cytoplasmic dynein heavy chain (From Topology)	T: C-terminal domain of cytoplasmic dynein heavy chain	F: Dynein_heavy_3rd	ECOD (1.6)
A	AAA_7_N	e4rh7A6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_7_N	ECOD (1.6)
A	AAA_8	e4rh7A8	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_8	ECOD (1.6)
A	AAA_6_N	e4rh7A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_6_N	ECOD (1.6)
A	Dynein_heavy_1st	e4rh7A12	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dynein_heavy_1st	ECOD (1.6)
A	AAA_5	e4rh7A4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_5	ECOD (1.6)
A	AAA_9_N	e4rh7A10	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_9_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.920.20	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22597	Dynein heavy chain, ATPase lid domain (DYN_lid)	Dynein heavy chain, ATPase lid domain	Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head ...	Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head with six AAA-domains, a coiled-coil stalk with a microtubule binding domain (MTBD) and a linker [1-5] This entry represents the lid domain found at the C-terminal of the third AAA+ ATPase domain in dyneins [1-5].	Domain
A	PF18198	Dynein heavy chain AAA lid domain (AAA_lid_11)	Dynein heavy chain AAA lid domain	This family represents the AAA lid domain found neat the C-terminal region of dynein heavy chain.	Domain
A	PF12775	P-loop containing dynein motor region (AAA_7)	P-loop containing dynein motor region	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliophathies. Dyneins share a conserved motor domain that couples cycles of ATP hydr ...	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliophathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs) [1].	Domain
A	PF12774	Hydrolytic ATP binding site of dynein motor region (AAA_6)	Hydrolytic ATP binding site of dynein motor region	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydro ...	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6) [1]. This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis [2]. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site [1].	Domain
A	PF12781	ATP-binding dynein motor region (AAA_9)	ATP-binding dynein motor region	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydro ...	This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk [1].	Domain
A	PF18199	Dynein heavy chain C-terminal domain (Dynein_C)	Dynein heavy chain C-terminal domain	This family represents the C-terminal domain of dynein heavy chain. This domain is a complex structure comprising six alpha-helices and an incomplete six-stranded antiparallel beta-barrel. The shape of this domain is distinctively flat, spreading ove ...	This family represents the C-terminal domain of dynein heavy chain. This domain is a complex structure comprising six alpha-helices and an incomplete six-stranded antiparallel beta-barrel. The shape of this domain is distinctively flat, spreading over the AAA1, AAA5 and AAA6 domain [3].	Domain
A	PF21264	Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain (DYNC2H1_AAA_dom)	Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain	This domain is found in Cytoplasmic dynein 2 heavy chain 1 from humans (DYNC2H1) and similar sequences from eukaryotes. Dynein-2 is essential for the dynamic remodelling of the ciliary proteome and is associated with human skeletal ciliopathies. DYNC ...	This domain is found in Cytoplasmic dynein 2 heavy chain 1 from humans (DYNC2H1) and similar sequences from eukaryotes. Dynein-2 is essential for the dynamic remodelling of the ciliary proteome and is associated with human skeletal ciliopathies. DYNC2H1, one of its specific components, is the motor-domain- containing heavy chain. This protein consists of a compact N-terminal region, an elongated tail and a C-terminal AAA+ motor domain. There are two copies of this protein in the complex, each adopting a different configuration, which contributes to the asymmetry of Dynein-2. This entry covers one of the six motor's ring AAA+ domains (ATPases associated with various cellular activities) [1,2].	Domain
A	PF12780	P-loop containing dynein motor region D4 (AAA_8)	P-loop containing dynein motor region D4	The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...	The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor [1].	Domain
A	PF12777	Microtubule-binding stalk of dynein motor (MT)	Microtubule-binding stalk of dynein motor	the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...	the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [1].	Domain
A	PF03028	Dynein heavy chain region D6 P-loop domain (Dynein_heavy)	Dynein heavy chain region D6 P-loop domain	This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved i ...	This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains [1]. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1	cytoskeletal motor activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding cytoskeletal motor activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding dynein light intermediate chain binding protein binding microtubule motor activity polypeptide conformation or assembly isomerase activity isomerase activity minus-end-directed microtubule motor activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity dynein intermediate chain binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cilium-dependent cell motility cellular process microtubule-based movement microtubule-based process cilium movement involved in cell motility cilium movement cell motility cilium or flagellum-dependent cell motility developmental process dorsal/ventral pattern formation multicellular organism development multicellular organismal process anatomical structure development pattern specification process cilium-dependent cell motility cellular process microtubule-based movement microtubule-based process cilium movement involved in cell motility cilium movement cell motility cilium or flagellum-dependent cell motility developmental process dorsal/ventral pattern formation multicellular organism development multicellular organismal process anatomical structure development pattern specification process regionalization animal organ development kidney development renal system development system development protein localization localization cellular localization protein localization to cilium protein localization to organelle cellular macromolecule localization macromolecule localization cellular developmental process cell differentiation in spinal cord nervous system development generation of neurons central nervous system neuron differentiation neurogenesis spinal cord development central nervous system development neuron differentiation cell differentiation ventral spinal cord development spinal cord motor neuron differentiation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of smoothened signaling pathway signal transduction positive regulation of cellular process regulation of smoothened signaling pathway regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation smoothened signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development anatomical structure morphogenesis appendage morphogenesis limb morphogenesis plasma membrane bounded cell projection organization cell projection organization transport intracellular transport intraciliary retrograde transport establishment of localization protein-containing complex localization cellular component organization organelle organization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular component organization or biogenesis cilium organization intraciliary transport organelle assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly non-motile cilium assembly cell projection assembly determination of bilateral symmetry determination of left/right symmetry left/right pattern formation specification of symmetry head development forebrain development brain development heart development coronary vasculature development vasculature development circulatory system development blood vessel development Golgi organization endomembrane system organization	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm apical part of cell extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle ciliary tip Golgi apparatus intracellular membrane-bounded organelle endomembrane system protein-containing complex cytoplasmic dynein complex catalytic complex dynein complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex cell periphery plasma membrane membrane 9+2 motile cilium motile cilium

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR026983	Dynein heavy chain	Family
A	IPR013602	Dynein heavy chain, linker	Domain
A	IPR041658	Dynein heavy chain AAA lid domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR042222	Dynein heavy chain, domain 2, N-terminal	Homologous Superfamily
A	IPR043160	Dynein heavy chain, C-terminal domain, barrel region	Homologous Superfamily
A	IPR035706	Dynein heavy chain, ATP-binding dynein motor region	Domain
A	IPR041228	Dynein heavy chain, C-terminal domain	Domain
A	IPR054354	Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domain	Domain
A	IPR003593	AAA+ ATPase domain	Domain
A	IPR042228	Dynein heavy chain, linker, subdomain 3	Homologous Superfamily
A	IPR035699	Dynein heavy chain, hydrolytic ATP-binding dynein motor region	Domain
A	IPR042219	Dynein heavy chain AAA lid domain superfamily	Homologous Superfamily
A	IPR024743	Dynein heavy chain, coiled coil stalk	Domain
A	IPR013594	Dynein heavy chain, tail	Domain
A	IPR043157	Dynein heavy chain, AAA1 domain, small subdomain	Homologous Superfamily
A	IPR049400	Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain	Domain
A	IPR004273	Dynein heavy chain region D6 P-loop domain	Domain
A	IPR024317	Dynein heavy chain, AAA module D4	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8NCM8	Jeune syndrome short rib-polydactyly syndrome short rib-polydactyly syndrome, Verma-Naumoff type breast cancer Saldino-Noonan syndrome asphyxiating thoracic dystrophy 3 breast carcinoma polydactyly osteogenesis imperfecta pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia short-rib thoracic dysplasia 6 with or without polydactyly cystic fibrosis invasive ductal breast carcinoma myocardial infarction osteosarcoma Jeune syndrome short rib-polydactyly syndrome short rib-polydactyly syndrome, Verma-Naumoff type breast cancer Saldino-Noonan syndrome asphyxiating thoracic dystrophy 3 breast carcinoma polydactyly osteogenesis imperfecta pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia short-rib thoracic dysplasia 6 with or without polydactyly cystic fibrosis invasive ductal breast carcinoma myocardial infarction osteosarcoma sinusitis atypical teratoid rhabdoid tumor heart disease malignant ependymoma nasopharyngeal carcinoma ovarian cancer psoriasis tuberculosis ciliopathy intellectual disability lung adenocarcinoma malignant mesothelioma

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.