[English] 日本語
Yorodumi
- EMDB-31142: Cryo-EM structure of human ABCB8 transporter in nucleotide bindin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31142
TitleCryo-EM structure of human ABCB8 transporter in nucleotide binding state
Map dataElectron density map
Sample
  • Cell: ABCB8
    • Protein or peptide: Mitochondrial potassium channel ATP-binding subunit
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / ABC-type peptide transporter activity / Mitochondrial ABC transporters / cell volume homeostasis / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / mitochondrial membrane / transmembrane transport / mitochondrial inner membrane ...mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / ABC-type peptide transporter activity / Mitochondrial ABC transporters / cell volume homeostasis / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / mitochondrial membrane / transmembrane transport / mitochondrial inner membrane / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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
Mitochondrial potassium channel ATP-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM
AuthorsLi SJ / Yang X
CitationJournal: Biochem Biophys Res Commun / Year: 2021
Title: Cryo-EM structure of human ABCB8 transporter in nucleotide binding state.
Authors: Shunjin Li / Yue Ren / Xuhang Lu / Yuequan Shen / Xue Yang /
Abstract: Human ATP-binding cassette transporter 8 of subfamily B (hABCB8) is an ABC transporter that located in the inner membrane of mitochondria. The ABCB8 is involved in the maturation of Fe-S and protects ...Human ATP-binding cassette transporter 8 of subfamily B (hABCB8) is an ABC transporter that located in the inner membrane of mitochondria. The ABCB8 is involved in the maturation of Fe-S and protects the heart from oxidative stress. Here, we present the cryo-EM structure of human ABCB8 binding with AMPPNP in inward-facing conformation with resolution of 4.1 Å. hABCB8 shows an open-inward conformation when ATP is bound. Unexpectedly, cholesterol molecules were identified in the transmembrane domain of hABCB8. Our results provide structural basis for the transport mechanism of the ABC transporter in mitochondria.
History
DepositionMar 29, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ehl
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31142.png

Downloads & links

-
Map

FileDownload / File: emd_31142.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron density map
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.24
Minimum - Maximum-0.45296374 - 1.3609467
Average (Standard dev.)0.0004283734 (±0.04350566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.4531.3610.000

-
Supplemental data

-
Sample components

-
Entire : ABCB8

EntireName: ABCB8
Components
  • Cell: ABCB8
    • Protein or peptide: Mitochondrial potassium channel ATP-binding subunit
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: ABCB8

SupramoleculeName: ABCB8 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Mitochondrial potassium channel ATP-binding subunit

MacromoleculeName: Mitochondrial potassium channel ATP-binding subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.628375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SLLRAVAHLR SQLWAHLPRA PLAPRWSPSA WCWVGGALLG PMVLSKHPHL CLVALCEAEE APPASSTPHV VGSRFNWKLF WQFLHPHLL VLGVAVVLAL GAALVNVQIP LLLGQLVEVV AKYTRDHVGS FMTESQNLST HLLILYGVQG LLTFGYLVLL S HVGERMAV ...String:
SLLRAVAHLR SQLWAHLPRA PLAPRWSPSA WCWVGGALLG PMVLSKHPHL CLVALCEAEE APPASSTPHV VGSRFNWKLF WQFLHPHLL VLGVAVVLAL GAALVNVQIP LLLGQLVEVV AKYTRDHVGS FMTESQNLST HLLILYGVQG LLTFGYLVLL S HVGERMAV DMRRALFSSL LRQDITFFDA NKTGQLVSRL TTDVQEFKSS FKLVISQGLR SCTQVAGCLV SLSMLSTRLT LL LMVATPA LMGVGTLMGS GLRKLSRQCQ EQIARAMGVA DEALGNVRTV RAFAMEQREE ERYGAELEAC RCRAEELGRG IAL FQGLSN IAFNCMVLGT LFIGGSLVAG QQLTGGDLMS FLVASQTVQR SMANLSVLFG QVVRGLSAGA RVFEYMALNP CIPL SGGCC VPKEQLRGSV TFQNVCFSYP CRPGFEVLKD FTLTLPPGKI VALVGQSGGG KTTVASLLER FYDPTAGVVM LDGRD LRTL DPSWLRGQVV GFISQEPVLF GTTIMENIRF GKLEASDEEV YTAAREANAH EFITSFPEGY NTVVGERGTT LSGGQK QRL AIARALIKQP TVLILDEATS ALDAESERVV QEALDRASAG RTVLVIAHRL STVRGAHCIV VMADGRVWEA GTHEELL KK GGLYAELIRR QALDAPRTAA PPPKKPEGPR SHQHKS

UniProtKB: Mitochondrial potassium channel ATP-binding subunit

-
Macromolecule #2: CHOLESTEROL

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

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.0 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

-
Image processing

Startup modelType of model: OTHER / Details: Ab-initio in CryoSPARC-2
Final reconstructionNumber images used: 43131
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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://pdbjlvh1.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