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- EMDB-31142: Cryo-EM structure of human ABCB8 transporter in nucleotide bindin... -

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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 / Mitochondrial ABC transporters / cell volume homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / mitochondrial membrane ...mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / Mitochondrial ABC transporters / cell volume homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / membrane
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 / Resolution: 4.1 Å
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-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

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

emd_31142.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
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
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.4531.3610.000

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Supplemental data

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Sample components

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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

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Supramolecule #1: ABCB8

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

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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

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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

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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

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Macromolecule #4: MAGNESIUM ION

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

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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

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

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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

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio in CryoSPARC-2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Number images used: 43131
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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