3QMZ

Crystal structure of the cytoplasmic dynein heavy chain motor domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth T]	SCOP2B Superfamily	GST C-terminal domain-like	8037552	3000305	SCOP2B (2022-06-29)
C [auth T]	SCOP2B Superfamily	Thioredoxin-like	8044378	3000031	SCOP2B (2022-06-29)
D [auth S]	SCOP2B Superfamily	GST C-terminal domain-like	8037552	3000305	SCOP2B (2022-06-29)
D [auth S]	SCOP2B Superfamily	Thioredoxin-like	8044378	3000031	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)
A	AAA_9_C	e3qmzA3	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	e3qmzA10	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_7_C	ECOD (1.6)
A	DYN1	e3qmzA9	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DYN1	ECOD (1.6)
A	KOG3595	e3qmzA7	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG3595	ECOD (1.6)
A	Dynein_heavy_2nd	e3qmzA4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Dynein_heavy_2nd	ECOD (1.6)
A	DHC_N2	e3qmzA1	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	AAA_7_N	e3qmzA6	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	e3qmzA2	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	e3qmzA8	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	e3qmzA11	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	e3qmzA5	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	e3qmzA12	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)
B	AAA_9_C	e3qmzB3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_9_C	ECOD (1.6)
B	AAA_7_C	e3qmzB10	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AAA_7_C	ECOD (1.6)
B	DYN1	e3qmzB9	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: DYN1	ECOD (1.6)
B	KOG3595	e3qmzB7	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG3595	ECOD (1.6)
B	Dynein_heavy_2nd	e3qmzB4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: Dynein_heavy_2nd	ECOD (1.6)
B	DHC_N2	e3qmzB1	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)
B	AAA_7_N	e3qmzB6	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)
B	AAA_8	e3qmzB2	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)
B	AAA_6_N	e3qmzB8	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)
B	Dynein_heavy_1st	e3qmzB11	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)
B	AAA_5	e3qmzB5	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)
B	AAA_9_N	e3qmzB12	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)
C [auth T]	GST_C_3	e3qmzT1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Glutathione S-transferase (GST)-C (From Topology)	T: Glutathione S-transferase (GST)-C	F: GST_C_3	ECOD (1.6)
C [auth T]	GST_N_5	e3qmzT2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)
D [auth S]	GST_C_3	e3qmzS1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Glutathione S-transferase (GST)-C (From Topology)	T: Glutathione S-transferase (GST)-C	F: GST_C_3	ECOD (1.6)
D [auth S]	GST_N_5	e3qmzS2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: GST_N_5	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	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, B	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, B	PF21499	DYN1, AAA+ ATPase lid domain (DYN1_lid)	DYN1, AAA+ ATPase lid domain	This entry includes dynein heavy chain (DYN1) from yeast, which is a cytoplasmic dynein that acts as a motor for intracellular retrograde motility of vesicles and organelles along microtubules. This entry represents the AAA+ ATPase lid domain [1-5].	Domain
A, B	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, B	PF08393	Dynein heavy chain, N-terminal region 2 (DHC_N2)	Dynein heavy chain, N-terminal region 2	-	Family
A, B	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, B	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
C [auth T], D [auth S]	PF14497	Glutathione S-transferase, C-terminal domain (GST_C_3)	Glutathione S-transferase, C-terminal domain	This domain is closely related to Pfam:PF00043.	Domain
C [auth T], D [auth S]	PF02798	Glutathione S-transferase, N-terminal domain (GST_N)	Glutathione S-transferase, N-terminal domain	Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity a ...	Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity and similarity not previously recognised); HSP26 family of stress-related proteins including auxin-regulated proteins in plants and stringent starvation proteins in E. coli (not known to have GST activity and similarity not previously recognised). The glutathione molecule binds in a cleft between the N- and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cytoplasmic dynein heavy chain	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 cytoskeletal motor activity minus-end-directed microtubule motor activity ATP-dependent activity 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 catalytic activity dynein intermediate chain binding	establishment of organelle localization cellular localization organelle transport along microtubule transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration along microtubule microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport establishment of organelle localization cellular localization organelle transport along microtubule transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration along microtubule microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process nuclear migration organelle fusion cellular component organization organelle organization nucleus organization karyogamy cellular component organization or biogenesis microtubule cytoskeleton organization spindle localization mitotic cell cycle establishment of mitotic spindle localization mitotic cell cycle process establishment of spindle localization cell cycle microtubule cytoskeleton organization involved in mitosis cytoskeleton organization cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation nuclear division mitotic sister chromatid segregation nuclear chromosome segregation chromosome segregation cytoplasmic microtubule organization supramolecular fiber organization establishment or maintenance of cell polarity establishment of spindle orientation establishment of cell polarity establishment of mitotic spindle orientation mitotic spindle organization spindle organization	cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber spindle aster astral microtubule intracellular membraneless organelle spindle microtubule cytoplasmic microtubule intracellular organelle cytoskeleton cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber spindle aster astral microtubule intracellular membraneless organelle spindle microtubule cytoplasmic microtubule intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton microtubule organizing center spindle pole body protein-containing complex cytoplasmic dynein complex catalytic complex dynein complex microtubule associated complex
C [auth T], D [auth S]	Glutathione-S-transferase	glutathione transferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	glutathione metabolic process modified amino acid metabolic process metabolic process cellular process sulfur compound metabolic process amide metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR026983	Dynein heavy chain	Family
A, B	IPR013602	Dynein heavy chain, linker	Domain
A, B	IPR035706	Dynein heavy chain, ATP-binding dynein motor region	Domain
A, B	IPR054354	Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domain	Domain
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR041658	Dynein heavy chain AAA lid domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR042228	Dynein heavy chain, linker, subdomain 3	Homologous Superfamily
A, B	IPR035699	Dynein heavy chain, hydrolytic ATP-binding dynein motor region	Domain
A, B	IPR042219	Dynein heavy chain AAA lid domain superfamily	Homologous Superfamily
A, B	IPR024743	Dynein heavy chain, coiled coil stalk	Domain
A, B	IPR013594	Dynein heavy chain, tail	Domain
A, B	IPR048404	DYN1, AAA+ ATPase lid domain	Domain
A, B	IPR043157	Dynein heavy chain, AAA1 domain, small subdomain	Homologous Superfamily
A, B	IPR042222	Dynein heavy chain, domain 2, N-terminal	Homologous Superfamily
A, B	IPR004273	Dynein heavy chain region D6 P-loop domain	Domain
A, B	IPR024317	Dynein heavy chain, AAA module D4	Domain
C [auth T], D [auth S]	IPR004046	Glutathione S-transferase, C-terminal	Domain
C [auth T], D [auth S]	IPR050213	Glutathione S-transferase superfamily	Family
C [auth T], D [auth S]	IPR010987	Glutathione S-transferase, C-terminal-like	Domain
C [auth T], D [auth S]	IPR036282	Glutathione S-transferase, C-terminal domain superfamily	Homologous Superfamily
C [auth T], D [auth S]	IPR004045	Glutathione S-transferase, N-terminal	Domain
C [auth T], D [auth S]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
C [auth T], D [auth S]	IPR040079	Glutathione transferase family	Family