7UT8

CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ATP-bound) during catalytic N2 reduction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 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

Structures of the nitrogenase complex prepared under catalytic turnover conditions.

Rutledge, H.L.Cook, B.D.Nguyen, H.P.M.Herzik Jr., M.A.Tezcan, F.A.

(2022) Science 377: 865-869

  • DOI: https://doi.org/10.1126/science.abq7641
  • Primary Citation of Related Structures:  
    7UT6, 7UT7, 7UT8, 7UT9, 7UTA, 8DPN

  • PubMed Abstract: 

    The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here, we report cryo-electron microscopy structures of the nitrogenase complex prepared under enzymatic turnover conditions. We observe that asymmetry governs all aspects of the nitrogenase mechanism, including ATP hydrolysis, protein-protein interactions, and catalysis. Conformational changes near the catalytic iron-molybdenum cofactor are correlated with the nucleotide-hydrolysis state of the enzyme.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C
492Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07328
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07329
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein gamma chain
E, F
290Azotobacter vinelandii DJMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
Explore P00459 
Go to UniProtKB:  P00459
Entity Groups  
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UniProt GroupP00459
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS (Subject of Investigation/LOI)
Query on ICS

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

Download Ideal Coordinates CCD File 
Q [auth E],
S [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
O [auth E]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
J [auth B],
M [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
P [auth E],
R [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM099813
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138206
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008326
National Aeronautic Space Administration (NASA, United States)United States80NSSC18M0093

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2024-02-14
    Changes: Data collection, Refinement description