Annotations: 7VGH

Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50B in the auto-inhibited E2P state

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e7vghB01	A: beta barrels	X: Fe-binding domain in prismane-like proteins	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03381	LEM3 (ligand-effect modulator 3) family / CDC50 family (CDC50)	LEM3 (ligand-effect modulator 3) family / CDC50 family	-	Family
B	PF16209	Phospholipid-translocating ATPase N-terminal (PhoLip_ATPase_N)	Phospholipid-translocating ATPase N-terminal	-	Family
B	PF16212	Phospholipid-translocating P-type ATPase C-terminal (PhoLip_ATPase_C)	Phospholipid-translocating P-type ATPase C-terminal	-	Family
B	PF00122	P-type ATPase actuator domain (E1-E2_ATPase)	P-type ATPase actuator domain	This entry describes the actuator (A) domain found in P-type ATPases (also known as E1-E2 ATPases). The A domain serves as a built-in protein phosphatase that functions to dephosphorylate the phosphorylated P domain. The A domain is the smallest of t ...	This entry describes the actuator (A) domain found in P-type ATPases (also known as E1-E2 ATPases). The A domain serves as a built-in protein phosphatase that functions to dephosphorylate the phosphorylated P domain. The A domain is the smallest of the three cytoplasmic domains. It consists of a distorted jellyroll structure and two short helices [1-2].	Domain
B	PF13246	P-type ATPase, cytoplasmic domain N (Cation_ATPase)	P-type ATPase, cytoplasmic domain N	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cell cycle control protein 50B	lipid carrier activity aminophospholipid flippase activity ATPase-coupled intramembrane lipid carrier activity flippase activity transporter activity intramembrane lipid carrier activity molecular carrier activity ATP-dependent activity	localization nitrogen compound transport transport macromolecule localization phospholipid transport lipid localization aminophospholipid transport lipid transport establishment of localization organophosphate ester transport regulation of protein exit from endoplasmic reticulum regulation of localization protein exit from endoplasmic reticulum establishment of protein localization localization nitrogen compound transport transport macromolecule localization phospholipid transport lipid localization aminophospholipid transport lipid transport establishment of localization organophosphate ester transport regulation of protein exit from endoplasmic reticulum regulation of localization protein exit from endoplasmic reticulum establishment of protein localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process positive regulation of establishment of protein localization positive regulation of protein transport establishment of localization in cell positive regulation of intracellular transport intracellular protein localization positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of transport biological regulation regulation of establishment of protein localization intracellular transport regulation of protein transport positive regulation of protein exit from endoplasmic reticulum positive regulation of transport protein transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport cellular process intracellular protein transport membrane organization phospholipid translocation lipid translocation regulation of membrane lipid distribution cellular component organization cellular component organization or biogenesis regulation of biological quality	cell periphery cellular anatomical structure plasma membrane membrane phospholipid-translocating ATPase complex protein-containing complex transporter complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle cell periphery cellular anatomical structure plasma membrane membrane phospholipid-translocating ATPase complex protein-containing complex transporter complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
B	Phospholipid-transporting ATPase IC	lipid carrier activity ATPase-coupled intramembrane lipid carrier activity transporter activity intramembrane lipid carrier activity molecular carrier activity ATP-dependent activity phosphatidylcholine floppase activity floppase activity phosphatidylcholine intramembrane carrier activity glycerophospholipid flippase activity phosphatidylserine flippase activity aminophospholipid flippase activity flippase activity phosphatidylcholine flippase activity lipid carrier activity ATPase-coupled intramembrane lipid carrier activity transporter activity intramembrane lipid carrier activity molecular carrier activity ATP-dependent activity phosphatidylcholine floppase activity floppase activity phosphatidylcholine intramembrane carrier activity glycerophospholipid flippase activity phosphatidylserine flippase activity aminophospholipid flippase activity flippase activity phosphatidylcholine flippase activity ion binding binding anion binding phosphatidylglycerol binding phospholipid binding lipid binding cardiolipin binding small molecule binding cation binding magnesium ion binding metal ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding phosphatidylserine floppase activity pyrophosphatase activity ATP hydrolysis 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	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process localization apical protein localization macromolecule localization intracellular protein localization developmental process multicellular organismal process cranial nerve formation cranial nerve morphogenesis nervous system development anatomical structure morphogenesis multicellular organism development nerve development vestibulocochlear nerve formation cranial nerve development vestibulocochlear nerve development vestibulocochlear nerve morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development system development oxoacid metabolic process steroid metabolic process carboxylic acid metabolic process organic acid metabolic process bile acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process lipid metabolic process transmembrane transport transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization mechanoreceptor differentiation inner ear receptor cell development cellular developmental process ear development sensory organ development animal organ development cell development inner ear receptor cell differentiation generation of neurons neurogenesis neuron differentiation cell differentiation inner ear development neuron development regulation of localization regulation of transport regulation of monoatomic ion transport chloride transport monoatomic anion transport regulation of monoatomic anion transport regulation of chloride transport inorganic anion transport regulation of cellular component organization plasma membrane bounded cell projection organization cell projection organization regulation of cell projection organization regulation of cell projection assembly plasma membrane bounded cell projection assembly regulation of cellular component biogenesis microvillus organization cellular component organization cellular component biogenesis regulation of microvillus organization regulation of plasma membrane bounded cell projection assembly regulation of microvillus assembly cellular component assembly microvillus assembly cellular component organization or biogenesis cell projection assembly regulation of plasma membrane bounded cell projection organization xenobiotic transmembrane transport xenobiotic transport organic anion transport carboxylic acid transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport organic acid transport monocarboxylic acid transport system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus membrane organization regulation of plasma membrane organization plasma membrane organization endomembrane system organization organelle organization Golgi organization phospholipid translocation phospholipid transport lipid translocation regulation of membrane lipid distribution regulation of biological quality organophosphate ester transport	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane intracellular anatomical structure cytoplasm cytosol phospholipid-translocating ATPase complex protein-containing complex transporter complex membrane-bounded organelle cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane intracellular anatomical structure cytoplasm cytosol phospholipid-translocating ATPase complex protein-containing complex transporter complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network cell projection stereocilium actin-based cell projection stereocilium bundle neuron projection cluster of actin-based cell projections plasma membrane bounded cell projection intracellular membraneless organelle nuclear body membraneless organelle endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005045	CDC50/LEM3 family	Family
B	IPR001757	P-type ATPase	Family
B	IPR044492	P-type ATPase, haloacid dehalogenase domain	Domain
B	IPR006539	P-type ATPase, subfamily IV	Family
B	IPR018303	P-type ATPase, phosphorylation site	PTM
B	IPR059000	P-type ATPase, A domain	Domain
B	IPR023298	P-type ATPase, transmembrane domain superfamily	Homologous Superfamily
B	IPR032631	P-type ATPase, N-terminal	Domain
B	IPR023214	HAD superfamily	Homologous Superfamily
B	IPR008250	P-type ATPase, A domain superfamily	Homologous Superfamily
B	IPR036412	HAD-like superfamily	Homologous Superfamily
B	IPR032630	P-type ATPase, C-terminal	Domain
B	IPR023299	P-type ATPase, cytoplasmic domain N	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: Q3MIR4	melanoma breast carcinoma interstitial cystitis malignant colon neoplasm ovarian cancer spina bifida cutaneous melanoma invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm ductal breast carcinoma in situ lung cancer nephrosclerosis Sjogren syndrome
B	: O43520	intrahepatic cholestasis cholestasis, intrahepatic, of pregnancy, 1 progressive familial intrahepatic cholestasis type 1 progressive familial intrahepatic cholestasis cholestasis benign recurrent intrahepatic cholestasis type 1 oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor esophageal adenocarcinoma intellectual disability invasive ductal breast carcinoma Malignant neoplasm of breast osteosarcoma intrahepatic cholestasis cholestasis, intrahepatic, of pregnancy, 1 progressive familial intrahepatic cholestasis type 1 progressive familial intrahepatic cholestasis cholestasis benign recurrent intrahepatic cholestasis type 1 oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor esophageal adenocarcinoma intellectual disability invasive ductal breast carcinoma Malignant neoplasm of breast osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease benign recurrent intrahepatic cholestasis dermatomyositis interstitial cystitis large cell medulloblastoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pituitary cancer spina bifida ductal breast carcinoma in situ gallbladder disease malignant ependymoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	P-type ATPase (P-ATPase)	Phospholipid-translocating ATPase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	P-type ATPase	P4-ATPase lipid flippase ATP8A1-CDC50A in the auto-inhibited E2P state

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	PHD	Parent Component: ASP : AA0033 : L-aspartic 4-phosphoric anhydride MOD:00042

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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.

7VGH | pdb_00007vgh