6SGE

Crystal structure of Human RHOB-GTP in complex with nanobody B6

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6sgea_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	RhoB	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6sgec_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	RhoB	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6sgeb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6sgeb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6sged1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6sged3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6sged2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057284	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057284	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	PF00071	e6sgeA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
C	PF00071	e6sgeC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
B	PF07686	e6sgeB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e6sgeD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, D	nAb B6	VH	Vicugna pacos (alpaca)	IGHV3-301, IGHJ601	V-DOMAIN VH	IG	VH	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV3	-	rho-related gtp-binding protein rhob	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, motil ...	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
B, D	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Rho-related GTP-binding protein RhoB	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 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 GDP 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	developmental process cellular developmental process cell differentiation cellular process cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell vacuolar transport developmental process cellular developmental process cell differentiation cellular process cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell vacuolar transport mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process multicellular organismal process positive regulation of locomotion regulation of cell motility regulation of cellular process endothelial cell migration positive regulation of biological process positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion positive regulation of cellular process regulation of biological process biological regulation epithelium migration regulation of locomotion positive regulation of endothelial cell migration blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development apoptotic process cell death programmed cell death negative regulation of cellular process negative regulation of biological process negative regulation of cell cycle regulation of cell cycle positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process cellular response to stimulus response to ionizing radiation response to stimulus cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus epithelium development endothelium development morphogenesis of an endothelium endothelial tube morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis epithelial tube morphogenesis signaling signal transduction cell communication cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress response to chemical protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport negative regulation of locomotion negative regulation of cell motility negative regulation of cell migration regulation of developmental process regulation of vasculature development positive regulation of developmental process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process cell adhesion small GTPase-mediated signal transduction Rho protein signal transduction intracellular signal transduction intracellular signaling cassette cellular component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization regulation of cellular component organization regulation of modification of synaptic structure regulation of synapse organization cell junction organization regulation of synapse structure or activity regulation of modification of postsynaptic structure synapse organization regulation of biological quality modification of synaptic structure modification of postsynaptic structure	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane endosome membrane endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome organelle membrane cell division site cleavage furrow plasma membrane region early endosome Schaffer collateral - CA1 synapse synapse nucleus
B, D	Nanobody B6	-	response to stimulus immune response immune system process adaptive immune response	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR003578	Small GTPase Rho	Family
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR001806	Small GTPase	Family
A, C	IPR005225	Small GTP-binding protein domain	Domain
B, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D	IPR003599	Immunoglobulin subtype	Domain
B, D	IPR013106	Immunoglobulin V-set domain	Domain
B, D	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P62745	systemic sclerosis myopathy osteosarcoma pituitary cancer sinusitis astrocytic tumor dermatomyositis Emery-Dreifuss muscular dystrophy gastric carcinoma juvenile dermatomyositis malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma ovarian cancer plasma cell myeloma systemic sclerosis myopathy osteosarcoma pituitary cancer sinusitis astrocytic tumor dermatomyositis Emery-Dreifuss muscular dystrophy gastric carcinoma juvenile dermatomyositis malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma ovarian cancer plasma cell myeloma subependymal giant cell astrocytoma ulcerative colitis atypical teratoid rhabdoid tumor diffuse scleroderma exocrine pancreatic carcinoma Gaucher disease large cell medulloblastoma malignant ependymoma medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma psoriasis Systemic Scleroderma urinary bladder cancer cystic fibrosis Down syndrome gastric cancer glioblastoma lung cancer 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 R01GM133198.