11UY | pdb_000011uy

Cryo-EM structure of dimeric Nitrogenase MoFe protein from Methanosarcina acetivorans

• PDB DOI: https://doi.org/10.2210/pdb11UY/pdb
• EM Map EMD-76071: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Methanosarcina acetivorans
• Mutation(s): No 


• Deposited: 2026-03-13 Released: 2026-10-07 
• Deposition Author(s): Kashyap, R., Antony, E.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Kashyap, R., Deere, T.M., Dhamad, A., Chanderban, M., Tokmina-Lukaszewska, M., Bothner, B., Lessner, D.J., Antony, E.

(2026) Nature 

• DOI: https://doi.org/10.1038/s41586-026-11116-z

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 226.07 kDa 
• Atom Count: 6,314 
• Modeled Residue Count: 814 
• Deposited Residue Count: 2,030 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	A [auth B], B [auth D]	456	Methanosarcina acetivorans	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for Q8TJ89 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TJ89  Go to UniProtKB:  Q8TJ89

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	C [auth A], D [auth C]	559	Methanosarcina acetivorans	Mutation(s): 0  EC: 1.18.6.1
UniProt
Find proteins for Q8TJ90 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TJ90  Go to UniProtKB:  Q8TJ90

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX	2.0-5936
MODEL REFINEMENT	PHENIX	2.0_5936

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Kashyap, R., Antony, E.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0020965

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release