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- PDB-7roq: Alternative Structure of Human ABCA1 -

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Basic information

Entry
Database: PDB / ID: 7roq
TitleAlternative Structure of Human ABCA1
ComponentsPhospholipid-transporting ATPase ABCA1
KeywordsLIPID TRANSPORT / ABCA1 atherosclerosis lipid export protein modeling transport mechanism
Function / homology
Function and homology information


sphingolipid floppase activity / regulation of high-density lipoprotein particle assembly / apolipoprotein A-I receptor activity / positive regulation of high-density lipoprotein particle assembly / Defective ABCA1 causes TGD / signal release / response to vitamin B3 / apolipoprotein A-I binding / intracellular cholesterol transport / platelet dense granule organization ...sphingolipid floppase activity / regulation of high-density lipoprotein particle assembly / apolipoprotein A-I receptor activity / positive regulation of high-density lipoprotein particle assembly / Defective ABCA1 causes TGD / signal release / response to vitamin B3 / apolipoprotein A-I binding / intracellular cholesterol transport / platelet dense granule organization / high-density lipoprotein particle binding / phospholipid transporter activity / floppase activity / response to laminar fluid shear stress / HDL assembly / protein transmembrane transport / phosphatidylserine floppase activity / peptide secretion / cellular response to cholesterol / phosphatidylcholine floppase activity / phospholipid homeostasis / phosphatidylcholine binding / phospholipid efflux / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / export across plasma membrane / lipoprotein biosynthetic process / P-type phospholipid transporter / regulation of Cdc42 protein signal transduction / syntaxin binding / phospholipid translocation / cholesterol efflux / endosomal transport / cholesterol binding / phagocytosis, engulfment / intracellular vesicle / lysosome organization / negative regulation of cholesterol storage / cellular response to cytokine stimulus / apolipoprotein binding / negative regulation of macrophage derived foam cell differentiation / endocytic vesicle / ATPase-coupled transmembrane transporter activity / cellular response to low-density lipoprotein particle stimulus / protein transmembrane transporter activity / protein secretion / positive regulation of cholesterol efflux / ABC-type transporter activity / phagocytic vesicle / cellular response to retinoic acid / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol metabolic process / cholesterol homeostasis / PPARA activates gene expression / adenylate cyclase-activating G protein-coupled receptor signaling pathway / small GTPase binding / cellular response to xenobiotic stimulus / ATPase binding / cellular response to lipopolysaccharide / basolateral plasma membrane / endosome / G protein-coupled receptor signaling pathway / membrane raft / external side of plasma membrane / intracellular membrane-bounded organelle / signaling receptor binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter A / ABC-2 family transporter protein / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CHOLESTEROL / Chem-POV / Phospholipid-transporting ATPase ABCA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsAller, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL128203 United States
CitationJournal: Cell / Year: 2017
Title: Structure of the Human Lipid Exporter ABCA1.
Authors: Hongwu Qian / Xin Zhao / Pingping Cao / Jianlin Lei / Nieng Yan / Xin Gong /
Abstract: ABCA1, an ATP-binding cassette (ABC) subfamily A exporter, mediates the cellular efflux of phospholipids and cholesterol to the extracellular acceptor apolipoprotein A-I (apoA-I) for generation of ...ABCA1, an ATP-binding cassette (ABC) subfamily A exporter, mediates the cellular efflux of phospholipids and cholesterol to the extracellular acceptor apolipoprotein A-I (apoA-I) for generation of nascent high-density lipoprotein (HDL). Mutations of human ABCA1 are associated with Tangier disease and familial HDL deficiency. Here, we report the cryo-EM structure of human ABCA1 with nominal resolutions of 4.1 Å for the overall structure and 3.9 Å for the massive extracellular domain. The nucleotide-binding domains (NBDs) display a nucleotide-free state, while the two transmembrane domains (TMDs) contact each other through a narrow interface in the intracellular leaflet of the membrane. In addition to TMDs and NBDs, two extracellular domains of ABCA1 enclose an elongated hydrophobic tunnel. Structural mapping of dozens of disease-related mutations allows potential interpretation of their diverse pathogenic mechanisms. Structural-based analysis suggests a plausible "lateral access" mechanism for ABCA1-mediated lipid export that may be distinct from the conventional alternating-access paradigm.
History
DepositionAug 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Remark 0THIS ENTRY 7ROQ REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN EMD-6724 ORIGINAL DATA ...THIS ENTRY 7ROQ REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN EMD-6724 ORIGINAL DATA DETERMINED BYAUTHOR: H.W.Qian,N.Yan,X.Gong

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Assembly

Deposited unit
A: Phospholipid-transporting ATPase ABCA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,0459
Polymers259,5131
Non-polymers3,5328
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phospholipid-transporting ATPase ABCA1 / ATP-binding cassette sub-family A member 1 / ATP-binding cassette transporter 1 / ABC-1 / ATP- ...ATP-binding cassette sub-family A member 1 / ATP-binding cassette transporter 1 / ABC-1 / ATP-binding cassette 1 / Cholesterol efflux regulatory protein


Mass: 259512.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCA1, ABC1, CERP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O95477, P-type phospholipid transporter

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Sugars , 3 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ABCA1 / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 790156 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314273
ELECTRON MICROSCOPYf_angle_d0.64319414
ELECTRON MICROSCOPYf_dihedral_angle_d6.3992021
ELECTRON MICROSCOPYf_chiral_restr0.052283
ELECTRON MICROSCOPYf_plane_restr0.0052444

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