8IPS

Cryo-EM structure of heme transporter CydDC from Escherichia coli in the inward facing heme loading state

• PDB DOI: https://doi.org/10.2210/pdb8IPS/pdb
• EM Map EMD-35642: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 
• 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: 3.60 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 of 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.

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

Macromolecule Content

• Total Structure Weight: 130.56 kDa 
• Atom Count: 9,071 
• Modelled Residue Count: 1,161 
• Deposited Residue Count: 1,177 
• 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	589	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: ECBD_2709 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	588	Escherichia coli BL21(DE3)	Mutation(s): 0  Gene Names: ECBD_2708 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
HEM (Subject of Investigation/LOI)	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 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		ZD2021CY1001
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