8IPR | pdb_00008ipr

Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the outward facing ATP bound state

PDB DOI: https://doi.org/10.2210/pdb8IPR/pdb
EM Map EMD-35641: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Mycolicibacterium smegmatis
Expression System: Mycolicibacterium smegmatis
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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/procel/pwad022
Primary Citation of Related Structures:
8IPQ, 8IPR, 8IPS, 8IPT

Organizational Affiliation

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content

Total Structure Weight: 212.4 kDa
Atom Count: 14,894
Modeled Residue Count: 2,038
Deposited Residue Count: 2,038
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC	A, C [auth D]	504	Mycolicibacterium smegmatis	Mutation(s): 1 Gene Names: cydC Membrane Entity: Yes
UniProt
Find proteins for A4ZHS8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A4ZHS8 Go to UniProtKB: A4ZHS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4ZHS8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane ATP-binding protein ABC transporter cydD	B [auth C], D [auth E]	515	Mycolicibacterium smegmatis	Mutation(s): 1 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QXA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain L [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth E] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth E]	F [auth A], H [auth C], J [auth D], L [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain I [auth D] SDF format, chain K [auth E] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D] MOL2 format, chain K [auth E] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain I [auth D] mmCIF format, chain K [auth E]	E [auth A], G [auth C], I [auth D], K [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth E] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Zhu, C.

Li, J.

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