9D9U | pdb_00009d9u

Rhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductase Complex with an Oxidized P-cluster

• PDB DOI: https://doi.org/10.2210/pdb9D9U/pdb
• EM Map EMD-46680: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Rhodospirillum rubrum ATCC 11170
• Mutation(s): No 


• Deposited: 2024-08-21 Released: 2025-11-05 
• Deposition Author(s): Kreitler, D.F., Hu, G., North, J.A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Architecture, catalysis and regulation of methylthio-alkane reductase for bacterial sulfur acquisition from volatile organic compounds

Murali, S., Hu, G.B., Kreitler, D.F., Carriedo, A.A., Lewis, L.C., Fosu, S.A., Weaver, O.G., Buzas, E.M., Byerly, K.M., Yoshikuni, Y., McSweeney, S., Shafaat, H.S., North, J.A.

(2025) Nat Catal 8: 1072-1085

• DOI: https://doi.org/10.1038/s41929-025-01425-3

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 218.28 kDa 
• Atom Count: 12,701 
• Modeled Residue Count: 1,632 
• Deposited Residue Count: 1,970 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase	A, B	519	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: Rru_A0794 EC: 1.18.6.1 (PDB Primary Data), 1.18 (UniProt)
UniProt
Find proteins for Q2RW97 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RW97  Go to UniProtKB:  Q2RW97

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase	C, D	466	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: Rru_A0793 EC: 1.18.6.1 (PDB Primary Data), 1.18 (UniProt)
UniProt
Find proteins for Q2RW98 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RW98  Go to UniProtKB:  Q2RW98

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLF (Subject of Investigation/LOI)	E [auth C], F [auth D]	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE
RECONSTRUCTION	cryoSPARC	4.2.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Kreitler, D.F., Hu, G., North, J.A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	KP1607011
Department of Energy (DOE, United States)	United States	DE-SC0022091
Department of Energy (DOE, United States)	United States	DE-SC0024125

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release