7Y49 | pdb_00007y49

Cryo-EM Structure of apo mitochondrial ABC transporter ABCB10 from Biortus

• PDB DOI: https://doi.org/10.2210/pdb7Y49/pdb
• EM Map EMD-33604: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-06-14 Released: 2023-04-19 
• Deposition Author(s): Cao, S., Yang, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structures of mitochondrial ABC transporter ABCB10 in apo and biliverdin-bound form.

Cao, S., Yang, Y., He, L., Hang, Y., Yan, X., Shi, H., Wu, J., Ouyang, Z.

(2023) Nat Commun 14: 2030-2030

• PubMed: 37041204 
• DOI: https://doi.org/10.1038/s41467-023-37851-9
• Primary Citation Related Structures: 
  7Y48, 7Y49


• PubMed Abstract: 
  

  ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron transporter mitoferrin-1. Recently, it was found that ABCB10 is a mitochondrial biliverdin exporter. However, the molecular mechanism of biliverdin export by ABCB10 remains elusive. Here we report the cryo-EM structures of ABCB10 in apo (ABCB10-apo) and biliverdin-bound form (ABCB10-BV) at 3.67 Å and 2.85 Å resolution, respectively. ABCB10-apo adopts a wide-open conformation and may thus represent the apo form structure. ABCB10-BV forms a closed conformation and biliverdin situates in a hydrophobic pocket in one protomer and bridges the interaction through hydrogen bonds with the opposing one. We also identify cholesterols sandwiched by BVs and discuss the export dynamics based on these structural and biochemical observations.

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Organizational Affiliation: 
• Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng Western Road, 214437, Jiangyin, Jiangsu, China.
Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, 430030, Wuhan, Hubei Province, China.
Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, 430030, Wuhan, Hubei Province, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 67.18 kDa 
• Atom Count: 4,169 
• Modeled Residue Count: 565 
• Deposited Residue Count: 613 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family B member 10, mitochondrial	A	613	Homo sapiens	Mutation(s): 1  Gene Names: ABCB10 EC: 7.6.2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRK6 (Homo sapiens) Explore Q9NRK6  Go to UniProtKB:  Q9NRK6
PHAROS:  Q9NRK6 GTEx:  ENSG00000135776

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.67 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Cao, S., Yang, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2023-04-26
  Changes: Database references
• Version 1.2: 2024-04-10
  Changes: Data collection, Refinement description