8OIE

Iron Nitrogenase Complex from Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 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, F
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron-iron protein delta chain
B, G
115Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: anfGRCAP_rcc00587
EC: 1.18.6.1
UniProt
Find proteins for D5ANJ8 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5ANJ8 
Go to UniProtKB:  D5ANJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANJ8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron-iron protein, beta subunit
C, H
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
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein
D, E, I, J
275Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: anfHnifHRCAP_rcc00585
EC: 1.18.6.1
UniProt
Find proteins for D5ANJ6 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5ANJ6 
Go to UniProtKB:  D5ANJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANJ6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S5Q (Subject of Investigation/LOI)
Query on S5Q

Download Ideal Coordinates CCD File 
K [auth A],
U [auth F]
FeFe cofactor
C Fe8 S9
ARHQIUGQOSHZFD-UHFFFAOYSA-N
CLF (Subject of Investigation/LOI)
Query on CLF

Download Ideal Coordinates CCD File 
M [auth A],
W [auth H]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth J],
N [auth D],
R [auth E],
X [auth I]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth I],
Q [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
L [auth A],
V [auth F]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
AF3
Query on AF3

Download Ideal Coordinates CCD File 
DA [auth J],
P [auth D],
T [auth E],
Z [auth I]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth J],
O [auth D],
S [auth E],
Y [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1

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