11MY | pdb_000011my

Cryo-EM structure of trimeric Nitrogenase MoFe protein from Methanosarcina acetivorans bound to the NifI inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb11MY/pdb
EM Map EMD-75852: EMDB EMDataResource

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

Deposited: 2026-03-05 Released: 2026-09-23
Deposition Author(s): Kashyap, R., Antony, E.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of trimeric Nitrogenase MoFe protein from Methanosarcina acetivorans bound to the NifI inhibitor complex

Kashyap, R., Antony, E.

To be published.

Macromolecule Content

Total Structure Weight: 265.4 kDa
Atom Count: 12,873
Modeled Residue Count: 1,640
Deposited Residue Count: 2,365
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	A, 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TJ90
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	B, 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TJ89
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P-II family nitrogen regulatory protein	E	125	Methanosarcina acetivorans	Mutation(s): 0
UniProt
Find proteins for Q8TJ91 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TJ91 Go to UniProtKB: Q8TJ91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TJ91
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
P-II family nitrogen regulatory protein	F, G [auth J]	105	Methanosarcina acetivorans	Mutation(s): 0
UniProt
Find proteins for Q8TJ92 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TJ92 Go to UniProtKB: Q8TJ92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TJ92
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 I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
CLF (Subject of Investigation/LOI) Query on CLF Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain M [auth J] SDF format, chain K [auth F] MOL2 format, chain L [auth F] MOL2 format, chain M [auth J] MOL2 format, chain K [auth F] mmCIF format, chain L [auth F] mmCIF format, chain M [auth J] mmCIF format, chain K [auth F]	K [auth F], L [auth F], M [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth F] Focus chain L [auth F] Focus chain M [auth J] Interactions & Density Focus chain K [auth F] Focus chain L [auth F] Focus chain M [auth J]
HCA (Subject of Investigation/LOI) Query on HCA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]