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- EMDB-6724: Cryo-EM structure of human ABCA1 -

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Basic information

Entry
Database: EMDB / ID: EMD-6724
TitleCryo-EM structure of human ABCA1
Map data
Sample
  • Organelle or cellular component: Membrane protein
    • Protein or peptide: ATP-binding cassette sub-family A member 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmembrane transporter / TRANSPORT PROTEIN
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
Phospholipid-transporting ATPase ABCA1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsQian HW / Yan N / Gong X
Funding support China, 2 items
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, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJun 7, 2017-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5xjy
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7roq
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6724.png

Downloads & links

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Map

FileDownload / File: emd_6724.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.35362256 - 0.48452526
Average (Standard dev.)0.00023639337 (±0.011452604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.3540.4850.000

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Supplemental data

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Additional map: #1

Fileemd_6724_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane protein

EntireName: Membrane protein
Components
  • Organelle or cellular component: Membrane protein
    • Protein or peptide: ATP-binding cassette sub-family A member 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Membrane protein

SupramoleculeName: Membrane protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP-binding cassette sub-family A member 1

MacromoleculeName: ATP-binding cassette sub-family A member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 259.512984 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADYKDDDDK SGPDEVDASG RMACWPQLRL LLWKNLTFRR RQTCQLLLEV AWPLFIFLIL ISVRLSYPPY EQHECHFPNK AMPSAGTLP WVQGIICNAN NPCFRYPTPG EAPGVVGNFN KSIVARLFSD ARRLLLYSQK DTSMKDMRKV LRTLQQIKKS S SNLKLQDF ...String:
MADYKDDDDK SGPDEVDASG RMACWPQLRL LLWKNLTFRR RQTCQLLLEV AWPLFIFLIL ISVRLSYPPY EQHECHFPNK AMPSAGTLP WVQGIICNAN NPCFRYPTPG EAPGVVGNFN KSIVARLFSD ARRLLLYSQK DTSMKDMRKV LRTLQQIKKS S SNLKLQDF LVDNETFSGF LYHNLSLPKS TVDKMLRADV ILHKVFLQGY QLHLTSLCNG SKSEEMIQLG DQEVSELCGL PR EKLAAAE RVLRSNMDIL KPILRTLNST SPFPSKELAE ATKTLLHSLG TLAQELFSMR SWSDMRQEVM FLTNVNSSSS STQ IYQAVS RIVCGHPEGG GLKIKSLNWY EDNNYKALFG GNGTEEDAET FYDNSTTPYC NDLMKNLESS PLSRIIWKAL KPLL VGKIL YTPDTPATRQ VMAEVNKTFQ ELAVFHDLEG MWEELSPKIW TFMENSQEMD LVRMLLDSRD NDHFWEQQLD GLDWT AQDI VAFLAKHPED VQSSNGSVYT WREAFNETNQ AIRTISRFME CVNLNKLEPI ATEVWLINKS MELLDERKFW AGIVFT GIT PGSIELPHHV KYKIRMDIDN VERTNKIKDG YWDPGPRADP FEDMRYVWGG FAYLQDVVEQ AIIRVLTGTE KKTGVYM QQ MPYPCYVDDI FLRVMSRSMP LFMTLAWIYS VAVIIKGIVY EKEARLKETM RIMGLDNSIL WFSWFISSLI PLLVSAGL L VVILKLGNLL PYSDPSVVFV FLSVFAVVTI LQCFLISTLF SRANLAAACG GIIYFTLYLP YVLCVAWQDY VGFTLKIFA SLLSPVAFGF GCEYFALFEE QGIGVQWDNL FESPVEEDGF NLTTSVSMML FDTFLYGVMT WYIEAVFPGQ YGIPRPWYFP CTKSYWFGE ESDEKSHPGS NQKRISEICM EEEPTHLKLG VSIQNLVKVY RDGMKVAVDG LALNFYEGQI TSFLGHNGAG K TTTMSILT GLFPPTSGTA YILGKDIRSE MSTIRQNLGV CPQHNVLFDM LTVEEHIWFY ARLKGLSEKH VKAEMEQMAL DV GLPSSKL KSKTSQLSGG MQRKLSVALA FVGGSKVVIL DEPTAGVDPY SRRGIWELLL KYRQGRTIIL STHHMDEADV LGD RIAIIS HGKLCCVGSS LFLKNQLGTG YYLTLVKKDV ESSLSSCRNS SSTVSYLKKE DSVSQSSSDA GLGSDHESDT LTID VSAIS NLIRKHVSEA RLVEDIGHEL TYVLPYEAAK EGAFVELFHE IDDRLSDLGI SSYGISETTL EEIFLKVAEE SGVDA ETSD GTLPARRNRR AFGDKQSCLR PFTEDDAADP NDSDIDPESR ETDLLSGMDG KGSYQVKGWK LTQQQFVALL WKRLLI ARR SRKGFFAQIV LPAVFVCIAL VFSLIVPPFG KYPSLELQPW MYNEQYTFVS NDAPEDTGTL ELLNALTKDP GFGTRCM EG NPIPDTPCQA GEEEWTTAPV PQTIMDLFQN GNWTMQNPSP ACQCSSDKIK KMLPVCPPGA GGLPPPQRKQ NTADILQD L TGRNISDYLV KTYVQIIAKS LKNKIWVNEF RYGGFSLGVS NTQALPPSQE VNDAIKQMKK HLKLAKDSSA DRFLNSLGR FMTGLDTKNN VKVWFNNKGW HAISSFLNVI NNAILRANLQ KGENPSHYGI TAFNHPLNLT KQQLSEVALM TTSVDVLVSI CVIFAMSFV PASFVVFLIQ ERVSKAKHLQ FISGVKPVIY WLSNFVWDMC NYVVPATLVI IIFICFQQKS YVSSTNLPVL A LLLLLYGW SITPLMYPAS FVFKIPSTAY VVLTSVNLFI GINGSVATFV LELFTDNKLN NINDILKSVF LIFPHFCLGR GL IDMVKNQ AMADALERFG ENRFVSPLSW DLVGRNLFAM AVEGVVFFLI TVLIQYRFFI RPRPVNAKLS PLNDEDEDVR RER QRILDG GGQNDILEIK ELTKIYRRKR KPAVDRICVG IPPGECFGLL GVNGAGKSST FKMLTGDTTV TRGDAFLNKN SILS NIHEV HQNMGYCPQF DAITELLTGR EHVEFFALLR GVPEKEVGKV GEWAIRKLGL VKYGEKYAGN YSGGNKRKLS TAMAL IGGP PVVFLDEPTT GMDPKARRFL WNCALSVVKE GRSVVLTSHS MEECEALCTR MAIMVNGRFR CLGSVQHLKN RFGDGY TIV VRIAGSNPDL KPVQDFFGLA FPGSVLKEKH RNMLQYQLPS SLSSLARIFS ILSQSKKRLH IEDYSVSQTT LDQVFVN FA KDQSDDDHLK DLSLHKNQTV VDVAVLTSFL QDEKVKESYV LEGSDEVDAV EGSHHHHHHH HHH

UniProtKB: Phospholipid-transporting ATPase ABCA1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 790156
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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