7F47 | pdb_00007f47

Cryo-EM structure of Rhizobium etli MprF

• PDB DOI: https://doi.org/10.2210/pdb7F47/pdb
• EM Map EMD-31445: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rhizobium etli CFN 42
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2021-06-17 Released: 2022-06-22 
• Deposition Author(s): Nishimura, M., Hirano, H., Gill, C.P., Phan, C.N.K., Yamashita, K., Kobayashi, K., Kise, Y., Kusakizako, T., Itoh, Y., Nishizawa, T., Roy, H., Nureki, O.
• Funding Organization(s): Japan Science and Technology, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of Rhizobium etli MprF

Nishimura, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.56 kDa 
• Atom Count: 6,435 
• Modeled Residue Count: 830 
• Deposited Residue Count: 867 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical conserved protein	A	867	Rhizobium etli CFN 42	Mutation(s): 0  Gene Names: RHE_CH03486 Membrane Entity: Yes
UniProt
Find proteins for Q2K4J4 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2K4J4  Go to UniProtKB:  Q2K4J4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGW (Subject of Investigation/LOI)	B [auth A], C [auth A]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C40 H77 O10 P PAZGBAOHGQRCBP-HGWHEPCSSA-N
LYS	D [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Nishimura, M., Hirano, H., Gill, C.P., Phan, C.N.K., Yamashita, K., Kobayashi, K., Kise, Y., Kusakizako, T., Itoh, Y., Nishizawa, T., Roy, H., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR20E2
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R21AI144481-02
Japan Society for the Promotion of Science (JSPS)	Japan	20H03216

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Derived calculations
• Version 1.2: 2024-06-12
  Changes: Data collection, Refinement description
• Version 2.0: 2026-08-05
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary