8IPQ | pdb_00008ipq

Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the inward facing apo state

• PDB DOI: https://doi.org/10.2210/pdb8IPQ/pdb
• EM Map EMD-35640: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Mycolicibacterium smegmatis
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-03-14 Released: 2023-06-14 
• Deposition Author(s): Zhu, C., Li, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of a prokaryotic heme transporter CydDC.

Zhu, C., Shi, Y., Yu, J., Zhao, W., Li, L., Liang, J., Yang, X., Zhang, B., Zhao, Y., Gao, Y., Chen, X., Yang, X., Zhang, L., Guddat, L.W., Liu, L., Yang, H., Rao, Z., Li, J.

(2023) Protein Cell 14: 919-923

• PubMed: 37144855 
• DOI: https://doi.org/10.1093/procel/pwad022
• Primary Citation Related Structures: 
  8IPQ, 8IPR, 8IPS, 8IPT

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Organizational Affiliation: 
• Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China.
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 216.16 kDa 
• Atom Count: 14,456 
• Modeled Residue Count: 1,996 
• Deposited Residue Count: 2,092 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane ATP-binding protein ABC transporter cydD	A [auth B], C	515	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: cydD, NCTC7017_05649 EC: 3.6.3.25 Membrane Entity: Yes
UniProt
Find proteins for A0QXA6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QXA6  Go to UniProtKB:  A0QXA6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC	B [auth A], D	531	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: cydC, NCTC7017_05650 Membrane Entity: Yes
UniProt
Find proteins for A4ZHS8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A4ZHS8  Go to UniProtKB:  A4ZHS8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Zhu, C., Li, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA1300900
Ministry of Science and Technology (MoST, China)	China	2022YFC2302900
Other government		22ZR1441600
Other government		ZD2021CY1001
Other government		LG202101-01-08

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Data collection, Database references