8IPT | pdb_00008ipt

Cryo-EM structure of heme transporter CydDC from Escherichia coli in the occluded ATP bound state

• PDB DOI: https://doi.org/10.2210/pdb8IPT/pdb
• EM Map EMD-35643: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 258.27 kDa 
• Atom Count: 18,178 
• Modeled Residue Count: 2,322 
• Deposited Residue Count: 2,322 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC	A [auth C], C [auth D]	573	Escherichia coli	Mutation(s): 1  Gene Names: ECBD_2709 EC: 7.4.2 Membrane Entity: Yes
UniProt
Find proteins for P23886 (Escherichia coli (strain K12)) Explore P23886  Go to UniProtKB:  P23886

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD	B [auth A], D [auth E]	588	Escherichia coli BL21(DE3)	Mutation(s): 1  Gene Names: ECBD_2708 EC: 7.4.2 Membrane Entity: Yes
UniProt
Find proteins for P29018 (Escherichia coli (strain K12)) Explore P29018  Go to UniProtKB:  P29018

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth C], F [auth A], G [auth D], H [auth E]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

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

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	22ZR1441600
Other government		22ZR1441600
Other government		ZD2021CY001
Other government	China	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