7EHL | pdb_00007ehl

Cryo-EM structure of human ABCB8 transporter in nucleotide binding state

• PDB DOI: https://doi.org/10.2210/pdb7EHL/pdb
• EM Map EMD-31142: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-03-29 Released: 2021-05-05 
• Deposition Author(s): Li, S.J., Yang, X., Shen, Y.Q.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human ABCB8 transporter in nucleotide binding state.

Li, S., Ren, Y., Lu, X., Shen, Y., Yang, X.

(2021) Biochem Biophys Res Commun 557: 187-191

• PubMed: 33872987 
• DOI: https://doi.org/10.1016/j.bbrc.2021.04.007
• Primary Citation Related Structures: 
  7EHL


• PubMed 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 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.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China; College of Life Sciences, Nankai University, Tianjin 100094, China.
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China; College of Life Sciences, Nankai University, Tianjin 100094, China; Synergetic Innovation Center of Chemical Science and Engineering, Tianjin 300071, China.
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 149.86 kDa 
• Atom Count: 8,048 
• Modeled Residue Count: 1,126 
• Deposited Residue Count: 1,356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial potassium channel ATP-binding subunit	A, B	678	Homo sapiens	Mutation(s): 0  Gene Names: ABCB8, MABC1, MITOSUR Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUT2 (Homo sapiens) Explore Q9NUT2  Go to UniProtKB:  Q9NUT2
PHAROS:  Q9NUT2 GTEx:  ENSG00000197150

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], I [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
CLR	C [auth A], E [auth A], G [auth B], H [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
MG	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Li, S.J., Yang, X., Shen, Y.Q.

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Data collection, Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Data processing, Structure summary