[English] 日本語
Yorodumi
- EMDB-25803: The structure of human ABCA1 in digitonin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25803
TitleThe structure of human ABCA1 in digitonin
Map data
Sample
  • Complex: human ABCA1 in digitonin
    • Protein or peptide: ATP-binding cassette, sub-family A (ABC1), member 1
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHDL / cholesterol / Tangier Disease / ABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


lipid transporter activity / P-type phospholipid transporter / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
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. ...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
P-type phospholipid transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSun Y / Li X
Funding support United States, 2 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRR-53S-19 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135343 United States
CitationJournal: Nat Cardiovasc Res / Year: 2022
Title: Cholesterol efflux mechanism revealed by structural analysis of human ABCA1 conformational states.
Authors: Yingyuan Sun / Xiaochun Li /
Abstract: ATP-binding cassette transporter A1 (ABCA1) utilizes energy derived from ATP hydrolysis to export cholesterol and phospholipids from macrophages. ABCA1 plays a central role in the biosynthesis of ...ATP-binding cassette transporter A1 (ABCA1) utilizes energy derived from ATP hydrolysis to export cholesterol and phospholipids from macrophages. ABCA1 plays a central role in the biosynthesis of high-density lipoprotein (HDL), which mediates reverse cholesterol transport and prevents detrimental lipid deposition. Mutations in ABCA1 cause Tangier disease characterized by a remarkable reduction in the amount of HDL in blood. Here we present cryo-electron microscopy structures of human ABCA1 in ATP-bound and nucleotide-free states. Structural comparison reveals that ATP molecules pull the nucleotide-binding domains together, inducing movements of transmembrane helices 1, 2, 7 and 8 through a series of salt-bridge interactions. Subsequently, extracellular domains (ECDs) undergo a rotation and introduce conformational changes in the ECD-transmembrane interface. In addition, while we observe a sterol-like molecule in ECDs, no such density was observed in the structure of an HDL-deficiency mutant ABCA1, demonstrating the physiological importance of ECDs and a putative interaction mode between ABCA1 and its lipid acceptors. Thus, these structures, along with cholesterol efflux assays, advance the understanding ABCA1-mediated reverse cholesterol transport.
History
DepositionDec 22, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7tc0
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25803.png

Downloads & links

-
Map

FileDownload / File: emd_25803.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 269.44 Å		0.84 Å/pix.
x 320 pix.
= 269.44 Å		0.84 Å/pix.
x 320 pix.
= 269.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.031510767 - 0.08806774
Average (Standard dev.)0.00030669247 (±0.002008915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 269.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8420.8420.842
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z269.440269.440269.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0320.0880.000

-
Supplemental data

-
Additional map: focused refinement of the ECDs

Fileemd_25803_additional_1.map
Annotationfocused refinement of the ECDs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25803_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25803_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human ABCA1 in digitonin

EntireName: human ABCA1 in digitonin
Components
  • Complex: human ABCA1 in digitonin
    • Protein or peptide: ATP-binding cassette, sub-family A (ABC1), member 1
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: human ABCA1 in digitonin

SupramoleculeName: human ABCA1 in digitonin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

-
Macromolecule #1: ATP-binding cassette, sub-family A (ABC1), member 1

MacromoleculeName: ATP-binding cassette, sub-family A (ABC1), member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 255.654984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MACWPQLRLL LWKNLTFRRR QTCQLLLEVA WPLFIFLILI SVRLSYPPYE QHECHFPNKA MPSAGTLPWV QGIICNANNP CFRYPTPGE APGVVGNFNK SIVARLFSDA RRLLLYSQKD TSMKDMRKVL RTLQQIKKSS SNLKLQDFLV DNETFSGFLY H NLSLPKST ...String:
MACWPQLRLL LWKNLTFRRR QTCQLLLEVA WPLFIFLILI SVRLSYPPYE QHECHFPNKA MPSAGTLPWV QGIICNANNP CFRYPTPGE APGVVGNFNK SIVARLFSDA RRLLLYSQKD TSMKDMRKVL RTLQQIKKSS SNLKLQDFLV DNETFSGFLY H NLSLPKST VDKMLRADVI LHKVFLQGYQ LHLTSLCNGS KSEEMIQLGD QEVSELCGLP REKLAAAERV LRSNMDILKP IL RTLNSTS PFPSKELAEA TKTLLHSLGT LAQELFSMRS WSDMRQEVMF LTNVNSSSSS TQIYQAVSRI VCGHPEGGGL KIK SLNWYE DNNYKALFGG NGTEEDAETF YDNSTTPYCN DLMKNLESSP LSRIIWKALK PLLVGKILYT PDTPATRQVM AEVN KTFQE LAVFHDLEGM WEELSPKIWT FMENSQEMDL VRMLLDSRDN DHFWEQQLDG LDWTAQDIVA FLAKHPEDVQ SSNGS VYTW REAFNETNQA IRTISRFMEC VNLNKLEPIA TEVWLINKSM ELLDERKFWA GIVFTGITPG SIELPHHVKY KIRMDI DNV ERTNKIKDGY WDPGPRADPF EDMRYVWGGF AYLQDVVEQA IIRVLTGTEK KTGVYMQQMP YPCYVDDIFL RVMSRSM PL FMTLAWIYSV AVIIKGIVYE KEARLKETMR IMGLDNSILW FSWFISSLIP LLVSAGLLVV ILKLGNLLPY SDPSVVFV F LSVFAVVTIL QCFLISTLFS RANLAAACGG IIYFTLYLPY VLCVAWRDYV GFTLKIFASL LSPVAFGFGC EYFALFEEQ GIGVQWDNLF ESPVEEDGFN LTTSVSMMLF DTFLYGVMTW YIEAVFPGQY GIPRPWYFPC TKSYWFGEES DEKSHPGSNQ KRISEICME EEPTHLKLGV SIQNLVKVYR DGMKVAVDGL ALNFYEGQIT SFLGHNGAGK TTTMSILTGL FPPTSGTAYI L GKDIRSEM STIRQNLGVC PQHNVLFDML TVEEHIWFYA RLKGLSEKHV KAEMEQMALD VGLPSSKLKS KTSQLSGGMQ RK LSVALAF VGGSKVVILD EPTAGVDPYS RRGIWELLLK YRQGRTIILS THHMDEADVL GDRIAIISHG KLCCVGSSLF LKN QLGTGY YLTLVKKDVE SSLSSCRNSS STVSYLKKED SVSQSSSDAG LGSDHESDTL TIDVSAISNL IRKHVSEARL VEDI GHELT YVLPYEAAKE GAFVELFHEI DDRLSDLGIS SYGISETTLE EIFLKVAEES GVDAETSDGT LPARRNRRAF GDKQS CLRP FTEDDAADPN DSDIDPESRE TDLLSGMDGK GSYQVKGWKL TQQQFVALLW KRLLIARRSR KGFFAQIVLP AVFVCI ALV FSLIVPPFGK YPSLELQPWM YNEQYTFVSN DAPEDTGTLE LLNALTKDPG FGTRCMEGNP IPDTPCQAGE EEWTTAP VP QTIMDLFQNG NWTMQNPSPA CQCSSDKIKK MLPVCPPGAG GLPPPQRKQN TADILQDLTG RNISDYLVKT YVQIIAKS L KNKIWVNEFR YGGFSLGVSN TQALPPSQEV NDAIKQMKKH LKLAKDSSAD RFLNSLGRFM TGLDTKNNVK VWFNNKGWH AISSFLNVIN NAILRANLQK GENPSHYGIT AFNHPLNLTK QQLSEVALMT TSVDVLVSIC VIFAMSFVPA SFVVFLIQER VSKAKHLQF ISGVKPVIYW LSNFVWDMCN YVVPATLVII IFICFQQKSY VSSTNLPVLA LLLLLYGWSI TPLMYPASFV F KIPSTAYV VLTSVNLFIG INGSVATFVL ELFTDNKLNN INDILKSVFL IFPHFCLGRG LIDMVKNQAM ADALERFGEN RF VSPLSWD LVGRNLFAMA VEGVVFFLIT VLIQYRFFIR PRPVNAKLSP LNDEDEDVRR ERQRILDGGG QNDILEIKEL TKI YRRKRK PAVDRICVGI PPGECFGLLG VNGAGKSSTF KMLTGDTTVT RGDAFLNKNS ILSNIHEVHQ NMGYCPQFDA ITEL LTGRE HVEFFALLRG VPEKEVGKVG EWAIRKLGLV KYGEKYAGNY SGGNKRKLST AMALIGGPPV VFLDEPTTGM DPKAR RFLW NCALSVVKEG RSVVLTSHSM EECEALCTRM AIMVNGRFRC LGSVQHLKNR FGDGYTIVVR IAGSNPDLKP VQDFFG LAF PGSVLKEKHR NMLQYQLPSS LSSLARIFSI LSQSKKRLHI EDYSVSQTTL DQVFVNFAKD QSDDDHLKDL SLHKNQT VV DVAVLTSFLQ DEKVKESYVG DYKDDDDK

UniProtKB: P-type phospholipid transporter

-
Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 618045
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more