1MA9 | pdb_00001ma9

Crystal structure of the complex of human vitamin D binding protein and rabbit muscle actin

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
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1ma9b1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Actin/HSP70	Actin	(Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
A	d1ma9a1	All alpha proteins	Serum albumin-like	Serum albumin-like	Serum albumin-like	Vitamin D binding protein	(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)
B	SCOP2B Superfamily	Actin-like ATPases	8040506	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8040509	3000092	SCOP2B (2022-06-29)
A	SCOP2 Family	Serum albumin-like	8031038	4001428	SCOP2 (2022-06-29)
A	SCOP2 Family	Serum albumin-like	8031039	4001428	SCOP2 (2022-06-29)
A	SCOP2 Family	Serum albumin-like	8031040	4001428	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Serum albumin-like	8043416	3001552	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Serum albumin-like	8043417	3001552	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Serum albumin-like	8043418	3001552	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Hexokinase_2	e1ma9B1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Hexokinase_2	ECOD (develop294)
A	Ion_trans_2	e1ma9A1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
A	MPI_cupin_dom	e1ma9A3	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: MPI_cupin_dom	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	2.30.36.70	Mainly Beta	Roll	Actin	Chain A, domain 2	CATH (4.3.0)
B	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
A	1.10.246.10	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09164	Vitamin D binding protein, domain III (VitD-bind_III)	Vitamin D binding protein, domain III	Members of this family are predominantly found in Vitamin D binding protein, and adopt a multi-helical structure. They are required for formation of an actin 'clamp', allowing the protein to bind to actin [1].	Domain
A	PF00273	Serum albumin family (Serum_albumin)	Serum albumin family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Actin, Alpha Skeletal Muscle	cytoskeletal protein binding titin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding hydrolase activity catalytic activity troponin I binding cytoskeletal motor activator activity cytoskeletal protein binding titin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding hydrolase activity catalytic activity troponin I binding cytoskeletal motor activator activity cytoskeletal motor regulator activity molecular function activator activity molecular function regulator activity magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding myosin heavy chain binding myosin binding tropomyosin binding calcium-dependent protein binding identical protein binding actin monomer binding actin binding	developmental process mesenchyme migration multicellular organismal process mesenchyme morphogenesis animal organ development mesenchyme development tissue development tissue morphogenesis anatomical structure morphogenesis tissue migration anatomical structure development animal organ morphogenesis myotube cell development skeletal muscle fiber development developmental process mesenchyme migration multicellular organismal process mesenchyme morphogenesis animal organ development mesenchyme development tissue development tissue morphogenesis anatomical structure morphogenesis tissue migration anatomical structure development animal organ morphogenesis myotube cell development skeletal muscle fiber development cellular developmental process skeletal muscle tissue development cell development muscle cell differentiation myotube differentiation striated muscle tissue development muscle structure development skeletal muscle organ development striated muscle cell development muscle cell development cell differentiation cellular process muscle tissue development muscle organ development striated muscle cell differentiation regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular component assembly involved in morphogenesis skeletal myofibril assembly membraneless organelle assembly cellular component organization cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly actin filament-based process cellular component organization or biogenesis skeletal muscle thin filament assembly actin cytoskeleton organization actomyosin structure organization organelle assembly actin filament organization organelle organization myofibril assembly anatomical structure formation involved in morphogenesis supramolecular fiber organization cytoskeleton organization protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization protein-containing complex assembly actin filament bundle organization actin filament bundle assembly	intracellular anatomical structure skeletal muscle myofibril intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cell projection intracellular anatomical structure skeletal muscle myofibril intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cytoskeleton actin filament bundle actin cytoskeleton actomyosin stress fiber contractile actin filament bundle polymeric cytoskeletal fiber actin filament protein-containing complex filamentous actin cell body striated muscle thin filament myofilament sarcomere actin-based cell projection filopodium
A	Vitamin D-binding protein	vitamin binding binding vitamin D binding steroid binding lipid binding small molecule binding cytoskeletal protein binding actin binding protein binding vitamin transmembrane transporter activity transporter activity transmembrane transporter activity D3 vitamins binding calcidiol binding	localization transport vitamin transport establishment of localization response to nutrient levels response to stimulus steroid metabolic process primary metabolic process metabolic process cellular process vitamin D metabolic process lipid metabolic process	cellular anatomical structure extracellular region extracellular space blood microparticle membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure extracellular region extracellular space blood microparticle membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle vesicle extracellular membrane-bounded organelle cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR020902	Actin/actin-like conserved site	Conserved Site
B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
B	IPR004001	Actin, conserved site	Conserved Site
B	IPR004000	Actin family	Family
A	IPR000213	Vitamin D-binding protein	Family
A	IPR015247	Vitamin D binding protein, domain III	Domain
A	IPR020857	Serum albumin, conserved site	Conserved Site
A	IPR000264	ALB/AFP/VDB	Family
A	IPR014760	Serum albumin, N-terminal	Domain
A	IPR020858	Serum albumin-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P02774	hepatic encephalopathy rheumatoid arthritis acute liver failure multiple sclerosis hepatic coma toxic shock syndrome schizophrenia Liver Cirrhosis, Experimental cirrhosis of liver Graves disease hypoparathyroidism lung benign neoplasm acute kidney failure pancreatic intraductal papillary-mucinous neoplasm drug-induced liver injury hepatic encephalopathy rheumatoid arthritis acute liver failure multiple sclerosis hepatic coma toxic shock syndrome schizophrenia Liver Cirrhosis, Experimental cirrhosis of liver Graves disease hypoparathyroidism lung benign neoplasm acute kidney failure pancreatic intraductal papillary-mucinous neoplasm drug-induced liver injury renal osteodystrophy rickets hypophosphatemia lung carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia injury nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	HIC	Parent Component: HIS RESID: AA0317 PSI-MOD : 1'-methyl-L-histidine MOD:00322

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.