8PBB

CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the iron nitrogenase complex.

Schmidt, F.V.Schulz, L.Zarzycki, J.Prinz, S.Oehlmann, N.N.Erb, T.J.Rebelein, J.G.

(2024) Nat Struct Mol Biol 31: 150-158

  • DOI: https://doi.org/10.1038/s41594-023-01124-2
  • Primary Citation of Related Structures:  
    8OIE, 8PBB

  • PubMed Abstract: 

    Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO 2 ) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO 2 , but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF 3 -stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [Fe 8 S 9 C-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.


  • Organizational Affiliation

    Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase protein alpha chain
A, C
535Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: anfD
UniProt
Find proteins for D5ANJ7 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5ANJ7 
Go to UniProtKB:  D5ANJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANJ7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron-iron protein, beta subunit
B, D
460Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: anfKRCAP_rcc00588
EC: 1.18.6.1
UniProt
Find proteins for D5ANJ9 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5ANJ9 
Go to UniProtKB:  D5ANJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANJ9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.1
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)Germany446841743

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Database references