8DPN | pdb_00008dpn

CryoEM structure of Azotobacter vinelandii nitrogenase MoFeP during catalytic N2 reduction

PDB DOI: https://doi.org/10.2210/pdb8DPN/pdb
EM Map EMD-27639: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Azotobacter vinelandii DJ
Mutation(s): No

Deposited: 2022-07-15 Released: 2022-08-17
Deposition Author(s): Rutledge, H.L., Cook, B., Tezcan, F.A., Herzik, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Aeronautic Space Administration (NASA, United States)

Experimental Data Snapshot

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

Starting Model: experimental
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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

PubMed: 35901182 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abq7641
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 233.24 kDa
Atom Count: 16,067
Modeled Residue Count: 1,998
Deposited Residue Count: 2,030
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein alpha chain	A, C	492	Azotobacter vinelandii DJ	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii) Explore P07328 Go to UniProtKB: P07328
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07328
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, D	523	Azotobacter vinelandii DJ	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii) Explore P07329 Go to UniProtKB: P07329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07329
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICS (Subject of Investigation/LOI) Query on ICS Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], J [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
CLF (Subject of Investigation/LOI) Query on CLF Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain G [auth B] MOL2 format, chain L [auth D] MOL2 format, chain G [auth B] mmCIF format, chain L [auth D] mmCIF format, chain G [auth B]	G [auth B], L [auth D]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
HCA (Subject of Investigation/LOI) Query on HCA Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A]	E [auth A], I [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain H [auth B]	H [auth B], K [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM099813
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138206
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008326
National Aeronautic Space Administration (NASA, United States)	United States	80NSSC18M0093