7EHL

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.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2021.04.007
Primary Citation of 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.

Organizational Affiliation

State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China; College of Life Sciences, Nankai University, Tianjin 100094, China.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	C [auth A], E [auth A], G [auth B], H [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]