6RZB

Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to microtubules

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)
B	SCOP2B Superfamily	Tubulin nucleotide-binding domain-like	8044258	3001758	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tubulin C-terminal domain-like	8036011	3001732	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)
C	MT	e6rzbC1	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	Tubulin_C	e6rzbA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: Tubulin C-terminal domain-like (From Topology)	T: Tubulin C-terminal domain-like	F: Tubulin_C	ECOD (1.6)
A	Tubulin	e6rzbA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
B	Tubulin_C	e6rzbB2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: Tubulin C-terminal domain-like (From Topology)	T: Tubulin C-terminal domain-like	F: Tubulin_C	ECOD (1.6)
B	Tubulin	e6rzbB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	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	PF00091	Tubulin/FtsZ family, GTPase domain (Tubulin)	Tubulin/FtsZ family, GTPase domain	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ...	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.	Domain
A	PF03953	Tubulin C-terminal domain (Tubulin_C)	Tubulin C-terminal domain	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tub ...	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).	Domain
B	PF00091	Tubulin/FtsZ family, GTPase domain (Tubulin)	Tubulin/FtsZ family, GTPase domain	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ...	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.	Domain
B	PF03953	Tubulin C-terminal domain (Tubulin_C)	Tubulin C-terminal domain	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tub ...	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	MKIAA0325 protein	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 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 catalytic activity	cellular process cell division establishment of organelle localization cellular localization transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration cellular component biogenesis cellular component organization cellular process cell division establishment of organelle localization cellular localization transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly non-membrane-bounded organelle assembly cellular component organization or biogenesis microtubule-based movement microtubule-based process cilium movement stress granule assembly microtubule cytoskeleton organization spindle localization establishment of spindle localization cell cycle cytoskeleton organization cell cycle process regulation of localization regulation of biological process biological regulation metaphase chromosome alignment chromosome localization nuclear chromosome segregation regulation of metaphase plate congression establishment of chromosome localization chromosome segregation positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process positive regulation of spindle assembly positive regulation of cell cycle process regulation of cell cycle positive regulation of cellular process spindle organization regulation of cell cycle process positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization positive regulation of cell cycle regulation of spindle assembly regulation of organelle assembly regulation of microtubule cytoskeleton organization positive regulation of organelle assembly regulation of mitotic spindle organization mitotic cell cycle microtubule cytoskeleton organization involved in mitosis mitotic spindle organization mitotic cell cycle process cytoplasmic microtubule organization supramolecular fiber organization multicellular organismal process homeostatic process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process metabolic process regulation of multicellular organismal process regulation of metabolic process regulation of transport positive regulation of transport regulation of cellular localization positive regulation of intracellular transport regulation of intracellular transport retrograde axonal transport axonal transport axo-dendritic transport microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport	membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cytoplasm somatodendritic compartment cell body neuronal cell body membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cytoplasm somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection protein-containing complex cytoplasmic dynein complex catalytic complex dynein complex cytoskeleton intracellular non-membrane-bounded organelle microtubule associated complex microtubule cytoskeleton non-membrane-bounded organelle actin-based cell projection filopodium neuron projection cytoplasm axon cytoplasm cytoplasmic region plasma membrane bounded cell projection cytoplasm cell periphery cell cortex centrosome microtubule organizing center manchette polymeric cytoskeletal fiber cytoplasmic microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex
A	Tubulin alpha-1B chain	structural constituent of cytoskeleton structural molecule activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding structural constituent of cytoskeleton structural molecule activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding pyrophosphatase activity GTPase 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	cellular process cell cycle mitotic cell cycle cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cellular component organization or biogenesis cytoskeleton organization	intracellular anatomical structure cytoplasm cellular anatomical entity polymeric cytoskeletal fiber intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle
B	Tubulin beta chain	structural constituent of cytoskeleton structural molecule activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding structural constituent of cytoskeleton structural molecule activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding pyrophosphatase activity GTPase 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	cellular process cell cycle mitotic cell cycle cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cellular component organization or biogenesis cytoskeleton organization	intracellular anatomical structure cytoplasm cellular anatomical entity polymeric cytoskeletal fiber intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR026983	Dynein heavy chain	Family
C	IPR013602	Dynein heavy chain, linker	Domain
C	IPR041658	Dynein heavy chain AAA lid domain	Domain
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR042222	Dynein heavy chain, domain 2, N-terminal	Homologous Superfamily
C	IPR043160	Dynein heavy chain, C-terminal domain, barrel region	Homologous Superfamily
C	IPR035706	Dynein heavy chain, ATP-binding dynein motor region	Domain
C	IPR041228	Dynein heavy chain, C-terminal domain	Domain
C	IPR054354	Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domain	Domain
C	IPR003593	AAA+ ATPase domain	Domain
C	IPR041466	Dynein heavy chain, AAA 5 extension domain	Domain
C	IPR042228	Dynein heavy chain, linker, subdomain 3	Homologous Superfamily
C	IPR035699	Dynein heavy chain, hydrolytic ATP-binding dynein motor region	Domain
C	IPR042219	Dynein heavy chain AAA lid domain superfamily	Homologous Superfamily
C	IPR024743	Dynein heavy chain, coiled coil stalk	Domain
C	IPR013594	Dynein heavy chain, tail	Domain
C	IPR043157	Dynein heavy chain, AAA1 domain, small subdomain	Homologous Superfamily
C	IPR004273	Dynein heavy chain region D6 P-loop domain	Domain
C	IPR024317	Dynein heavy chain, AAA module D4	Domain
A	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
A	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
A	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
A	IPR017975	Tubulin, conserved site	Conserved Site
A	IPR002452	Alpha tubulin	Family
A	IPR000217	Tubulin	Family
A	IPR023123	Tubulin, C-terminal	Homologous Superfamily
A	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
A	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily
B	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
B	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
B	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
B	IPR017975	Tubulin, conserved site	Conserved Site
B	IPR000217	Tubulin	Family
B	IPR023123	Tubulin, C-terminal	Homologous Superfamily
B	IPR002453	Beta tubulin	Family
B	IPR013838	Beta tubulin, autoregulation binding site	Binding Site
B	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
B	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily