1MA9

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
B	SCOP2B Superfamily	Actin-like ATPases	8040506	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8040509	3000092	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	Serum_albumin	e1ma9A1	A: alpha complex topology	X: Serum albumin-like (From Topology)	H: Serum albumin-like (From Topology)	T: Serum albumin-like	F: Serum_albumin	ECOD (1.6)
A	VitD-bind_III	e1ma9A3	A: alpha complex topology	X: Serum albumin-like (From Topology)	H: Serum albumin-like (From Topology)	T: Serum albumin-like	F: VitD-bind_III	ECOD (1.6)
B	Actin_1st	e1ma9B1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_1st	ECOD (1.6)
B	Actin_2nd	e1ma9B2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.246.10	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
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)

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
B	PF00022	Actin (Actin)	Actin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Vitamin D-binding protein	vitamin binding binding organic cyclic compound 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 vitamin binding binding organic cyclic compound 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 fat-soluble vitamin metabolic process steroid metabolic process organic hydroxy compound metabolic process primary metabolic process vitamin D metabolic process vitamin metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process small molecule metabolic process localization transport vitamin transport establishment of localization fat-soluble vitamin metabolic process steroid metabolic process organic hydroxy compound metabolic process primary metabolic process vitamin D metabolic process vitamin metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process small molecule metabolic process lipid metabolic process	extracellular region extracellular space cellular anatomical entity blood microparticle membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle extracellular region extracellular space cellular anatomical entity blood microparticle membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen 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
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 organic cyclic compound 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 muscle structure development skeletal muscle organ development muscle cell development cell differentiation cellular process muscle tissue development muscle organ development striated muscle cell differentiation regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process cellular component assembly involved in morphogenesis non-membrane-bounded organelle assembly skeletal myofibril assembly cellular component organization cellular component biogenesis striated muscle cell development 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 cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle cell projection intracellular anatomical structure skeletal muscle myofibril cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

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 acute kidney failure lung benign neoplasm drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm hepatic encephalopathy rheumatoid arthritis acute liver failure multiple sclerosis hepatic coma toxic shock syndrome schizophrenia Liver Cirrhosis, Experimental cirrhosis of liver Graves disease hypoparathyroidism acute kidney failure lung benign neoplasm drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm 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 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.