3RYF | pdb_00003ryf

GTP-Tubulin: RB3 Stathmin-like domain complex

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d3ryfe1	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Stathmin	Stathmin	Stathmin 4	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d3ryfe2	Artifacts	Tags	Tags	Tags	N-terminal Tags	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d3ryfd1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
D	d3ryfd2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
B	d3ryfb1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
B	d3ryfb2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
C	d3ryfc1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
C	d3ryfc2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
A	d3ryfa1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
A	d3ryfa2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Stathmin	8041515	3001374	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)
E	Stathmin	e3ryfE1	A: extended segments	X: Stathmin (From Topology)	H: Stathmin (From Topology)	T: Stathmin	F: Stathmin	ECOD (1.6)
D	Tubulin_C	e3ryfD1	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)
D	Tubulin	e3ryfD2	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	e3ryfB1	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	e3ryfB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
C	Tubulin_C	e3ryfC3	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)
C	Tubulin	e3ryfC4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
A	Tubulin_C	e3ryfA3	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	e3ryfA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	6.10.280.30	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.2.0)
D	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.2.0)
D	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
D	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.2.0)
B	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.2.0)
B	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
B	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.2.0)
C	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.2.0)
C	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
C	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.2.0)
A	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.2.0)
A	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.2.0)
A	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF00836	Stathmin family (Stathmin)	Stathmin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	Stathmin-4	cytoskeletal protein binding protein binding binding tubulin binding	regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of biological process regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization biological regulation regulation of microtubule-based process regulation of organelle organization cellular component organization organelle organization microtubule polymerization or depolymerization cellular process microtubule-based process regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of biological process regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization biological regulation regulation of microtubule-based process regulation of organelle organization cellular component organization organelle organization microtubule polymerization or depolymerization cellular process microtubule-based process cellular component organization or biogenesis cytoskeleton organization regulation of microtubule cytoskeleton organization cellular component disassembly protein-containing complex organization protein-containing complex disassembly microtubule depolymerization supramolecular fiber organization protein depolymerization developmental process multicellular organismal process plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system growth cone axon cell projection distal axon neuron projection membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth
B, D	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 purine nucleotide binding anion binding heterocyclic compound 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 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	microtubule-based process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber intracellular membraneless organelle intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton
A, C	Tubulin alpha chain	hydrolase activity catalytic activity protein-containing complex binding binding cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding protein heterodimerization activity protein dimerization activity guanyl nucleotide binding GTP binding hydrolase activity catalytic activity protein-containing complex binding binding cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding protein heterodimerization activity protein dimerization activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding structural constituent of cytoskeleton structural molecule activity	multicellular organismal process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells developmental process cerebellum morphogenesis cerebellar cortex morphogenesis head development hindbrain morphogenesis animal organ development brain development multicellular organismal process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells developmental process cerebellum morphogenesis cerebellar cortex morphogenesis head development hindbrain morphogenesis animal organ development brain development nervous system development cerebellar cortex development anatomical structure morphogenesis multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development behavior system process learning or memory nervous system process cognition memory protein polymerization protein-containing complex organization microtubule cytoskeleton organization microtubule polymerization cellular component organization cellular component biogenesis organelle organization microtubule polymerization or depolymerization cellular component assembly protein-containing complex assembly cellular process microtubule-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion startle response neuromuscular process response to external stimulus forebrain development pallium development cerebral cortex development telencephalon development brain morphogenesis forebrain morphogenesis animal organ morphogenesis response to acid chemical response to oxygen-containing compound response to nitrogen compound response to L-glutamate response to amino acid cellular developmental process neurogenesis gliogenesis glial cell differentiation cell differentiation establishment of organelle localization cellular localization organelle transport along microtubule transport intracellular transport establishment of localization localization organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation smoothened signaling pathway cell communication signal transduction adult locomotory behavior adult behavior locomotory behavior regulation of cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality response to light stimulus learning visual learning visual behavior associative learning response to radiation response to abiotic stimulus sperm motility reproductive process cilium movement involved in cell motility cilium or flagellum-dependent cell motility cilium-dependent cell motility flagellated sperm motility cilium movement cell motility exploration behavior locomotory exploration behavior establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization intracellular protein transport response to mechanical stimulus biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process neuron apoptotic process apoptotic process cell death programmed cell death microtubule organizing center organization centrosome cycle cell cycle cell cycle process generation of neurons central nervous system neuron differentiation neuron differentiation pyramidal neuron differentiation dentate gyrus development hippocampus development limbic system development motor behavior neuron migration cell migration cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis plasma membrane bounded cell projection organization neuron projection arborization neuron development response to peptide response to cytokine response to tumor necrosis factor	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection neuromuscular junction synapse cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection neuromuscular junction synapse cell junction endosome intracellular vesicle intracellular membrane-bounded organelle recycling endosome endomembrane system intracellular organelle cytoplasmic vesicle vesicle membraneless organelle intracellular membraneless organelle chromosome condensed chromosome polymeric cytoskeletal fiber axoneme axonemal microtubule cytoplasmic microtubule plasma membrane bounded cell projection cytoplasm cytoskeleton supramolecular polymer supramolecular complex microtubule cytoskeleton ciliary plasm cytoplasmic region supramolecular fiber microtubule cell periphery plasma membrane membrane cytoplasmic ribonucleoprotein granule ribonucleoprotein granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR000956	Stathmin family	Family
E	IPR030514	Stathmin, conserved site	Conserved Site
E	IPR036002	Stathmin superfamily	Homologous Superfamily
B, D	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
B, D	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
B, D	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
B, D	IPR017975	Tubulin, conserved site	Conserved Site
B, D	IPR000217	Tubulin	Family
B, D	IPR023123	Tubulin, C-terminal	Homologous Superfamily
B, D	IPR002453	Beta tubulin	Family
B, D	IPR013838	Beta tubulin, autoregulation binding site	Binding Site
B, D	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
B, D	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily
A, C	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
A, C	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
A, C	IPR000217	Tubulin	Family
A, C	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
A, C	IPR017975	Tubulin, conserved site	Conserved Site
A, C	IPR023123	Tubulin, C-terminal	Homologous Superfamily
A, C	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
A, C	IPR002452	Alpha tubulin	Family
A, C	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359