6TQR

The crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PapD-like	8061616	3002067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PapD-like	8061616	3002067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PapD-like	8061616	3002067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PapD-like	8061616	3002067	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	PF00635	e6tqrA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00635	ECOD (1.6)
B	PF00635	e6tqrB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00635	ECOD (1.6)
C	PF00635	e6tqrC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00635	ECOD (1.6)
D	PF00635	e6tqrD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00635	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00635	MSP (Major sperm protein) domain (Motile_Sperm)	MSP (Major sperm protein) domain	Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins.	Domain
E, F	PF10457	Cholesterol-capturing domain (MENTAL)	Cholesterol-capturing domain	Human meta-static lymph node (MLN) 64 is a late endosomal membrane protein, and carries this MENTAL (MLN64N-terminal) domain at its N-terminus. The domain is composed of four trans-membrane helices with three short intervening loops [1]. The function ...	Human meta-static lymph node (MLN) 64 is a late endosomal membrane protein, and carries this MENTAL (MLN64N-terminal) domain at its N-terminus. The domain is composed of four trans-membrane helices with three short intervening loops [1]. The function of the domain is to capture cholesterol and pass it to the associated START domain Pfam:PF01852 for transfer to a cytosolic acceptor protein or membrane. In mammals, the MENTAL domain is involved in the localisation of MLN64 and MENTHO in late endosomes, and also in homo-and of hetero-interactions of these two proteins [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Vesicle-associated membrane protein-associated protein A	protein binding binding protein domain specific binding protein heterodimerization activity protein dimerization activity FFAT motif binding cytoskeletal protein binding microtubule binding tubulin binding identical protein binding protein homodimerization activity cell adhesion molecule binding cadherin binding	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis vesicle budding from membrane cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport vesicle organization localization membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis vesicle budding from membrane cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport vesicle organization localization organelle organization establishment of localization in cell COPII-coated vesicle budding Golgi vesicle transport cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling negative regulation by host of viral genome replication biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle negative regulation by host of viral process modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process viral genome replication viral process biological process involved in interaction with symbiont positive regulation by host of viral process positive regulation by host of viral genome replication nitrogen compound transport ceramide transport amide transport macromolecule localization organic substance transport lipid localization lipid transport phospholipid transport organophosphate ester transport cholesterol transport sterol transport organic hydroxy compound transport sphingolipid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process lipid biosynthetic process sphingomyelin biosynthetic process phospholipid metabolic process organic substance metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process amide metabolic process phosphorus metabolic process sphingomyelin metabolic process membrane lipid metabolic process organonitrogen compound metabolic process cellular metabolic process amide biosynthetic process primary metabolic process sphingolipid metabolic process phospholipid biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process membrane lipid biosynthetic process lipid metabolic process endoplasmic reticulum-plasma membrane tethering membrane docking endoplasmic reticulum localization endoplasmic reticulum organization organelle localization by membrane tethering organelle localization endomembrane system organization protein localization protein localization to organelle cellular macromolecule localization protein localization to endoplasmic reticulum exit from host cell viral release from host cell biological process involved in interaction with host 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 organelle cellular anatomical entity vesicle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane membrane-bounded organelle organelle cellular anatomical entity vesicle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane intracellular vesicle lytic vacuole bounding membrane of organelle vesicle membrane cytoplasmic vesicle lysosome vacuolar membrane azurophil granule vacuole lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane cytoplasm secretory granule membrane cytosol cell periphery plasma membrane cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane Golgi membrane Golgi apparatus cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction
E, F	StAR-related lipid transfer protein 3	sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding sterol transfer activity lipid transporter activity lipid transfer activity transporter activity cholesterol transfer activity identical protein binding sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding sterol transfer activity lipid transporter activity lipid transfer activity transporter activity cholesterol transfer activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	vesicle localization establishment of organelle localization cellular localization transport establishment of vesicle localization vesicle tethering to endoplasmic reticulum establishment of localization vesicle targeting vesicle-mediated transport cellular component organization localization organelle localization establishment of localization in cell cellular process vesicle localization establishment of organelle localization cellular localization transport establishment of vesicle localization vesicle tethering to endoplasmic reticulum establishment of localization vesicle targeting vesicle-mediated transport cellular component organization localization organelle localization establishment of localization in cell cellular process cellular component organization or biogenesis vesicle tethering macromolecule localization organic substance transport lipid localization cholesterol transport lipid transport sterol transport organic hydroxy compound transport organic substance metabolic process primary metabolic process metabolic process lipid metabolic process organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process small molecule metabolic process mitochondrial transport cellular biosynthetic process lipid biosynthetic process C21-steroid hormone metabolic process cellular ketone metabolic process organic substance biosynthetic process progesterone metabolic process regulation of biological quality steroid biosynthetic process hormone biosynthetic process steroid hormone biosynthetic process olefinic compound biosynthetic process small molecule biosynthetic process progesterone biosynthetic process regulation of hormone levels cellular metabolic process biological regulation C21-steroid hormone biosynthetic process hormone metabolic process biosynthetic process organic cyclic compound biosynthetic process olefinic compound metabolic process ketone biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle organelle membrane contact site endoplasmic reticulum-endosome membrane contact site cytosol endosome membrane endosome membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle organelle membrane contact site endoplasmic reticulum-endosome membrane contact site cytosol endosome membrane endosome membrane intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome vesicle organelle membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR008962	PapD-like superfamily	Homologous Superfamily
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR000535	Major sperm protein (MSP) domain	Domain
A, B, C, D	IPR016763	Vesicle-associated membrane-protein-associated protein	Family
E, F	IPR000799	Steroidogenic acute regulatory protein-like	Family
E, F	IPR029867	StAR-related lipid transfer protein 3, C-terminal	Domain
E, F	IPR023393	START-like domain superfamily	Homologous Superfamily
E, F	IPR019498	MENTAL domain	Domain
E, F	IPR002913	START domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9P0L0	atypical teratoid rhabdoid tumor breast cancer invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma plasma cell myeloma tuberculosis bipolar disorder breast carcinoma large cell medulloblastoma malignant glioma osteosarcoma psoriasis botulism glioblastoma atypical teratoid rhabdoid tumor breast cancer invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma plasma cell myeloma tuberculosis bipolar disorder breast carcinoma large cell medulloblastoma malignant glioma osteosarcoma psoriasis botulism glioblastoma lymphoplasmacytic lymphoma medulloblastoma ovarian cancer subependymal giant cell astrocytoma
E, F	Pharos: Q14849	prostate cancer bipolar disorder inflammatory bowel disease rheumatoid arthritis cocaine use systemic lupus erythematosus Crohn disease ulcerative colitis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.