4HLQ | pdb_00004hlq

Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	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	Peptidase_M49	e4hlqA5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
C	Melibiase_C	e4hlqC5	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Melibiase_C	ECOD (v294.1)
E	Peptidase_M49	e4hlqE5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
G	Peptidase_M49	e4hlqG5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
I	Peptidase_M49	e4hlqI5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
B	RRM_1	e4hlqB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
D	RRM_1	e4hlqD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
F	RRM_1	e4hlqF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
H	RRM_1	e4hlqH1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
J	RRM_1	e4hlqJ1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.1310	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.472.80	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
C	1.10.8.1310	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.10.472.80	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
E	1.10.8.1310	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	1.10.472.80	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
G	1.10.8.1310	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
G	1.10.472.80	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
I	1.10.8.1310	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
I	1.10.472.80	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
J	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I	PF00566	Rab-GTPase-TBC domain (RabGAP-TBC)	Rab-GTPase-TBC domain	-	Family
B, D, F, H, J	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I	TBC1 domain family member 20	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development regulation of localization cellular localization regulation of cellular process transport positive regulation of biological process positive regulation of ER to Golgi vesicle-mediated transport vesicle-mediated transport localization intercellular transport establishment of localization in cell positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of ER to Golgi vesicle-mediated transport regulation of transport biological regulation intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport establishment of localization positive regulation of transport regulation of cellular localization cellular process Golgi vesicle transport cellular developmental process sensory organ development visual system development cell development cell morphogenesis epithelial cell differentiation eye morphogenesis lens morphogenesis in camera-type eye cell differentiation animal organ morphogenesis sensory system development camera-type eye morphogenesis lens fiber cell morphogenesis epithelium development eye development tissue development lens fiber cell development anatomical structure morphogenesis epithelial cell development sensory organ morphogenesis camera-type eye development lens fiber cell differentiation lens development in camera-type eye cellular component organization organelle organization lipid droplet organization cellular component organization or biogenesis virion assembly viral process viral life cycle positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity membrane organization vesicle budding from membrane vesicle cargo loading vesicle organization COPII-coated vesicle cargo loading COPII-coated vesicle budding spermatid development spermatid differentiation sexual reproduction spermatogenesis cellular component assembly involved in morphogenesis cellular process involved in reproduction in multicellular organism gamete generation cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly endomembrane system organization organelle assembly secretory granule organization multicellular organismal reproductive process male gamete generation anatomical structure formation involved in morphogenesis germ cell development acrosome assembly host-mediated activation of viral genome replication biological process involved in interspecies interaction between organisms host-mediated perturbation of viral genome replication host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process host-mediated activation of viral process regulation of viral process regulation by virus of viral protein levels in host cell positive regulation by virus of viral protein levels in host cell positive regulation of viral process regulation of biological quality Golgi organization	membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane nuclear membrane membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane nuclear membrane nucleus organelle envelope nuclear envelope endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
B, D, F, H, J	Ras-related protein Rab-1B	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 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 pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process regulation of cellular process positive regulation of glycoprotein metabolic process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process regulation of primary metabolic process regulation of glycoprotein metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process regulation of cellular component organization regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell Golgi vesicle transport establishment of protein localization protein transport macromolecule localization intracellular protein localization intracellular protein transport Golgi organization endomembrane system organization	cellular anatomical structure endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane cellular anatomical structure endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane membrane phagophore assembly site transport vesicle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane Golgi apparatus Golgi membrane bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I	IPR045913	GTPase-activating protein TBC20/Gyp8-like	Family
A, C, E, G, I	IPR035969	Rab-GAP-TBC domain superfamily	Homologous Superfamily
A, C, E, G, I	IPR000195	Rab-GAP-TBC domain	Domain
B, D, F, H, J	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F, H, J	IPR005225	Small GTP-binding domain	Domain
B, D, F, H, J	IPR001806	Small GTPase	Family
B, D, F, H, J	IPR050227	Ras-related protein Rab	Family
B, D, F, H, J	IPR057289	Rab1/Ypt1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I	Pharos: Q96BZ9	Warburg micro syndrome Warburg micro syndrome 4 cataract-intellectual disability-hypogonadism syndrome glioblastoma osteosarcoma coloboma large cell medulloblastoma ovarian cancer Warburg Sjo Fledelius syndrome microcephaly
B, D, F, H, J	Pharos: Q9H0U4	astrocytic tumor coronary artery disease ovarian carcinoma bipolar disorder gout prostate carcinoma breast carcinoma myocardial ischemia

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.