9NSV | pdb_00009nsv

CryoEM structure of ancestral nitrogenase MoFe-protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 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

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.

Shen, Y.Maggiolo, A.O.Zhang, T.Warmack, R.A.

(2025) Structure 33: 1484

  • DOI: https://doi.org/10.1016/j.str.2025.06.007
  • Primary Citation of Related Structures:  
    9N4V, 9N4W, 9N4X, 9N4Y, 9N59, 9N5A, 9NSV

  • PubMed Abstract: 

    Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.


  • Organizational Affiliation
    • Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase MoFe-protein alpha chain
A, C
493Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for C1DGZ7 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DGZ7 
Go to UniProtKB:  C1DGZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DGZ7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase MoFe-protein beta chain
B, D
523Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for C1DGZ8 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DGZ8 
Go to UniProtKB:  C1DGZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DGZ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS (Subject of Investigation/LOI)
Query on ICS

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF (Subject of Investigation/LOI)
Query on CLF

Download Ideal Coordinates CCD File 
G [auth B],
L [auth D]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
H [auth B],
K [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143836
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM152765

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-17
    Changes: Data collection, Database references