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- PDB-5xjy: Cryo-EM structure of human ABCA1 -

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Entry
Database: PDB / ID: 5xjy
TitleCryo-EM structure of human ABCA1
ComponentsATP-binding cassette sub-family A member 1
KeywordsTRANSPORT PROTEIN / membrane transporter
Function / homology
Function and homology information


sphingolipid floppase activity / positive regulation of high-density lipoprotein particle assembly / regulation of high-density lipoprotein particle assembly / apolipoprotein A-I receptor activity / signal release / response to laminar fluid shear stress / Defective ABCA1 causes TGD / intracellular cholesterol transport / phospholipid transfer activity / apolipoprotein A-I binding ...sphingolipid floppase activity / positive regulation of high-density lipoprotein particle assembly / regulation of high-density lipoprotein particle assembly / apolipoprotein A-I receptor activity / signal release / response to laminar fluid shear stress / Defective ABCA1 causes TGD / intracellular cholesterol transport / phospholipid transfer activity / apolipoprotein A-I binding / platelet dense granule organization / protein transmembrane transport / floppase activity / HDL assembly / high-density lipoprotein particle binding / phosphatidylserine floppase activity / lipoprotein biosynthetic process / phospholipid homeostasis / cellular response to cholesterol / ATPase-coupled intramembrane lipid carrier activity / phospholipid efflux / phosphatidylcholine floppase activity / reverse cholesterol transport / high-density lipoprotein particle assembly / phosphatidylcholine binding / cholesterol transfer activity / export across plasma membrane / P-type phospholipid transporter / syntaxin binding / response to vitamin B3 / regulation of Cdc42 protein signal transduction / cholesterol efflux / phospholipid translocation / lysosome organization / endosomal transport / negative regulation of cholesterol storage / cellular response to cytokine stimulus / intracellular vesicle / protein secretion / cholesterol binding / cholesterol metabolic process / negative regulation of macrophage derived foam cell differentiation / ATPase-coupled transmembrane transporter activity / positive regulation of cholesterol efflux / apolipoprotein binding / cellular response to low-density lipoprotein particle stimulus / transmembrane protein transporter activity / endocytic vesicle / ABC-type transporter activity / cellular response to retinoic acid / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol homeostasis / phagocytic vesicle / cellular response to xenobiotic stimulus / PPARA activates gene expression / small GTPase binding / ATPase binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to lipopolysaccharide / basolateral plasma membrane / endosome / membrane raft / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ACT-like domain / ABC transporter A / : / ABCA1-like, C-terminal R1 regulatory domain / 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 ...ACT-like domain / ABC transporter A / : / ABCA1-like, C-terminal R1 regulatory domain / 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
Phospholipid-transporting ATPase ABCA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsQian, H.W. / Yan, N. / Gong, X.
Funding support China, 2items
OrganizationGrant numberCountry
the Ministry of Science and Technology of China2015CB910101, 2016YFA0500402, 2014ZX09507003-006 and 2016YFA0501100 China
the National Natural Science Foundation of China31621092, 31630017, and 31611130036 China
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
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
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Revision 1.2Oct 9, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
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Structure visualization

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Assembly

Deposited unit
A: ATP-binding cassette sub-family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,9548
Polymers259,5131
Non-polymers2,4417
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ATP-binding cassette sub-family A member 1 / ATP-binding cassette transporter 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
#2: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-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
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/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)][b-D-Manp]{}[(6+1)][b-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.: 5
Source method: isolated from a genetically manipulated source
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
Has protein modificationY

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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: Membrane protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11rc3_2542: / Classification: refinement
EM softwareName: PHENIX / Category: model 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_d0.0113015
ELECTRON MICROSCOPYf_angle_d1.27917837
ELECTRON MICROSCOPYf_dihedral_angle_d10.9437655
ELECTRON MICROSCOPYf_chiral_restr0.0672180
ELECTRON MICROSCOPYf_plane_restr0.0092329

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