1Z9O | pdb_00001z9o

1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PapD-like	8061620	3002067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PapD-like	8061620	3002067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PapD-like	8061620	3002067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PapD-like	8061620	3002067	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PapD-like	8061620	3002067	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PapD-like	8061620	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	Sigma_1_2	e1z9oA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
B	Sigma_1_2	e1z9oB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
C	Sigma_1_2	e1z9oC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
D	Sigma_1_2	e1z9oD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
E	Sigma_1_2	e1z9oE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
F	Sigma_1_2	e1z9oF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	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 protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein binding binding protein domain specific binding protein heterodimerization activity protein dimerization activity FFAT motif binding cytoskeletal protein binding microtubule binding tubulin binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein-containing complex binding	membrane organization vesicle budding from membrane cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport cellular component organization vesicle organization localization organelle organization establishment of localization in cell cellular process membrane organization vesicle budding from membrane cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport cellular component organization vesicle organization localization organelle organization establishment of localization in cell cellular process cellular component organization or biogenesis COPII-coated vesicle budding Golgi vesicle transport nitrogen compound transport ceramide transport macromolecule localization lipid localization lipid transport phospholipid transport organophosphate ester transport cholesterol transport sterol transport organic hydroxy compound transport host-mediated suppression of viral genome replication biological process involved in interspecies interaction between organisms viral genome replication viral process viral life cycle host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process sphingolipid biosynthetic process lipid biosynthetic process primary metabolic process sphingolipid metabolic process sphingomyelin biosynthetic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process phosphorus metabolic process sphingomyelin metabolic process lipid metabolic process host-mediated activation of viral genome replication host-mediated perturbation of viral genome replication host-mediated activation of viral 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 to organelle intracellular protein localization protein localization to endoplasmic reticulum exit from host cell viral release from host cell biological process involved in interaction with host biological process involved in symbiotic interaction 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	cellular anatomical structure membrane membrane-bounded organelle organelle vesicle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane cellular anatomical structure membrane membrane-bounded organelle organelle vesicle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope nuclear envelope organelle membrane cell periphery plasma membrane cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm endoplasmic reticulum membrane Golgi membrane Golgi apparatus bounding membrane of organelle cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction perinuclear region of cytoplasm
G, H, I, J, K G, H, I, J, K, L	Oxysterol binding protein	sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding	localization transport macromolecule localization lipid localization lipid transport establishment of localization	membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cytosol cell periphery membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle cytosol cell periphery plasma membrane membrane late endosome organelle membrane contact site perinuclear endoplasmic reticulum perinuclear region of cytoplasm endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008962	PapD-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000535	Major sperm protein (MSP) domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR016763	Vesicle-associated membrane-protein-associated protein	Family
G, H, I, J, K G, H, I, J, K, L	IPR002110	Ankyrin repeat	Repeat
G, H, I, J, K G, H, I, J, K, L	IPR001849	Pleckstrin homology domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR018494	Oxysterol-binding protein, conserved site	Conserved Site
G, H, I, J, K G, H, I, J, K, L	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR037239	Oxysterol-binding protein superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR000648	Oxysterol-binding protein	Family
G, H, I, J, K G, H, I, J, K, L	IPR011993	PH-like domain superfamily	Homologous Superfamily

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.