7PLM | pdb_00007plm

CryoEM reconstruction of pyruvate ferredoxin oxidoreductase (PFOR) in anaerobic conditions


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7PLM

This is version 1.2 of the entry. See complete history

Literature

Oxygen-Sensitive Metalloprotein Structure Determination by Cryo-Electron Microscopy.

Cherrier, M.V.Vernede, X.Fenel, D.Martin, L.Arragain, B.Neumann, E.Fontecilla-Camps, J.C.Schoehn, G.Nicolet, Y.

(2022) Biomolecules 12

  • DOI: https://doi.org/10.3390/biom12030441
  • Primary Citation Related Structures: 
    7PLM

  • PubMed Abstract: 

    Metalloproteins are involved in key cell processes such as photosynthesis, respiration, and oxygen transport. However, the presence of transition metals (notably iron as a component of [Fe-S] clusters) often makes these proteins sensitive to oxygen-induced degradation. Consequently, their study usually requires strict anaerobic conditions. Although X-ray crystallography has been the method of choice for solving macromolecular structures for many years, recently electron microscopy has also become an increasingly powerful structure-solving technique. We have used our previous experience with cryo-crystallography to develop a method to prepare cryo-EM grids in an anaerobic chamber and have applied it to solve the structures of apoferritin and the 3 [Fe 4 S 4 ]-containing pyruvate ferredoxin oxidoreductase (PFOR) at 2.40 Å and 2.90 Å resolution, respectively. The maps are of similar quality to the ones obtained under air, thereby validating our method as an improvement in the structural investigation of oxygen-sensitive metalloproteins by cryo-EM.


  • Organizational Affiliation
    • Metalloproteins Unit, Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 270.76 kDa 
  • Atom Count: 18,225 
  • Modeled Residue Count: 2,354 
  • Deposited Residue Count: 2,464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyruvate:ferredoxin oxidoreductase
A, B
1,232Desulfocurvibacter africanusMutation(s): 0 
Gene Names: por
EC: 1.2.7.1
UniProt
Find proteins for P94692 (Desulfocurvibacter africanus)
Explore P94692 
Go to UniProtKB:  P94692
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94692
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
(Subject of Investigation/LOI)

Query on TPP



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4

Query on SF4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
Grenoble Instruct-ERIC Center (ISBG)FranceUMS 3518 CNRS-CEA-UGA-EMBL
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-10-LABX-49-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary