+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6724 | |||||||||
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Title | Cryo-EM structure of human ABCA1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information signal release / 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 / response to vitamin B3 / apolipoprotein A-I binding / intracellular cholesterol transport / platelet dense granule organization ...signal release / 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 / response to vitamin B3 / apolipoprotein A-I binding / intracellular cholesterol transport / platelet dense granule organization / phospholipid transporter activity / high-density lipoprotein particle binding / protein transmembrane transport / response to laminar fluid shear stress / phospholipid efflux / floppase activity / HDL assembly / peptide secretion / cholesterol transfer activity / reverse cholesterol transport / phosphatidylserine floppase activity / high-density lipoprotein particle assembly / lipoprotein biosynthetic process / cellular response to cholesterol / phospholipid homeostasis / phosphatidylcholine floppase activity / phosphatidylcholine binding / regulation of Cdc42 protein signal transduction / export across plasma membrane / P-type phospholipid transporter / cholesterol efflux / phospholipid translocation / syntaxin binding / cholesterol binding / endosomal transport / phagocytosis, engulfment / lysosome organization / intracellular vesicle / negative regulation of cholesterol storage / cellular response to cytokine stimulus / apolipoprotein binding / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / protein transmembrane transporter activity / endocytic vesicle / protein secretion / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / phagocytic vesicle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to retinoic acid / cholesterol metabolic process / cholesterol homeostasis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / PPARA activates gene expression / small GTPase binding / cellular response to xenobiotic stimulus / ATPase binding / basolateral plasma membrane / cellular response to lipopolysaccharide / endosome / membrane raft / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Qian HW / Yan N / Gong X | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6724.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-6724-v30.xml emd-6724.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_6724.png | 38.4 KB | ||
Others | emd_6724_additional.map.gz | 28.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6724 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6724 | HTTPS FTP |
-Related structure data
Related structure data | 5xjyMC 7roqM M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10798 (Title: Cryo-EM micrographs of human ABCA1 / Data size: 16.3 TB Data #1: The micrographs are the movie stacks (32 frames) after motion corrected with MotionCorr and binned 2-fold, resulting in a pixel size of 1.307 Å/pixel. [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6724.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.30654 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_6724_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Membrane protein
Entire | Name: Membrane protein |
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Components |
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-Supramolecule #1: Membrane protein
Supramolecule | Name: Membrane protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: ATP-binding cassette sub-family A member 1
Macromolecule | Name: ATP-binding cassette sub-family A member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 259.512984 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: N-ACETYL-D-GLUCOSAMINE
Macromolecule | Name: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 2 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
-Macromolecule #3: BETA-D-MANNOSE
Macromolecule | Name: BETA-D-MANNOSE / type: ligand / ID: 3 / Number of copies: 3 / Formula: BMA |
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Molecular weight | Theoretical: 180.156 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 790156 |