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- PDB-7ehl: Cryo-EM structure of human ABCB8 transporter in nucleotide bindin... -

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Basic information

Entry
Database: PDB / ID: 7ehl
TitleCryo-EM structure of human ABCB8 transporter in nucleotide binding state
ComponentsMitochondrial potassium channel ATP-binding subunit
KeywordsMEMBRANE PROTEIN / ABC transporter
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CHOLESTEROL / Mitochondrial potassium channel ATP-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi, S.J. / Yang, X. / Shen, Y.Q.
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 9, 2025Group: Data collection / Data processing / Structure summary
Category: em_3d_reconstruction / em_admin / pdbx_entry_details
Item: _em_3d_reconstruction.resolution / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_3d_reconstruction / em_admin / Data content type: EM metadata / EM metadata
Item: _em_3d_reconstruction.resolution / _em_admin.last_update

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Assembly

Deposited unit
A: Mitochondrial potassium channel ATP-binding subunit
B: Mitochondrial potassium channel ATP-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,86410
Polymers147,2572
Non-polymers2,6088
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mitochondrial potassium channel ATP-binding subunit / ATP-binding cassette sub-family B member 8 / mitochondrial / ABCB8 / Mitochondrial ATP-binding ...ATP-binding cassette sub-family B member 8 / mitochondrial / ABCB8 / Mitochondrial ATP-binding cassette 1 / M-ABC1 / Mitochondrial sulfonylurea-receptor / MITOSUR


Mass: 73628.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1, MITOSUR / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2
#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ABCB8 / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.1 Å / Num. of particles: 43131 / Symmetry type: POINT

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