12AH | pdb_000012ah

Cryo-EM structure of Nitrogenase MoFe protein from Methanosarcina acetivorans bound to the NifI inhibitor complex in C3 symmetry

PDB DOI: https://doi.org/10.2210/pdb12AH/pdb
EM Map EMD-76263: EMDB EMDataResource

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

Deposited: 2026-03-23 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: 2.97 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 Nitrogenase MoFe protein from Methanosarcina acetivorans bound to the NifI inhibitor complex in C3 symmetry

Kashyap, R., Antony, E.

To be published.

Macromolecule Content

Total Structure Weight: 914.67 kDa
Atom Count: 60,855
Modeled Residue Count: 7,724
Deposited Residue Count: 8,100
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase molybdenum-iron protein beta chain	A [auth B] B [auth D] C [auth M] D [auth N] E [auth W] A [auth B], B [auth D], C [auth M], D [auth N], E [auth W], F [auth X]	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase protein alpha chain	AA [auth p] G [auth e] H [auth q] Q [auth f] V [auth k] AA [auth p], G [auth e], H [auth q], Q [auth f], V [auth k], W [auth l]	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P-II family nitrogen regulatory protein	CA [auth s] DA [auth t] I [auth F] J [auth H] K [auth P] CA [auth s], DA [auth t], I [auth F], J [auth H], K [auth P], M [auth T], N [auth Z], P [auth b], T [auth i], U [auth j], Y [auth n], Z [auth o]	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

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
P-II family nitrogen regulatory protein	BA [auth r] L [auth Q] O [auth a] R [auth g] S [auth h] BA [auth r], L [auth Q], O [auth a], R [auth g], S [auth h], X [auth m]	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

Small Molecules

Ligands 5 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 XA [auth l] SDF format, chain WA [auth k] SDF format, chain PA [auth f] SDF format, chain MA [auth q] SDF format, chain IA [auth e] SDF format, chain DB [auth p] MOL2 format, chain XA [auth l] MOL2 format, chain WA [auth k] MOL2 format, chain PA [auth f] MOL2 format, chain MA [auth q] MOL2 format, chain IA [auth e] MOL2 format, chain DB [auth p] mmCIF format, chain XA [auth l] mmCIF format, chain WA [auth k] mmCIF format, chain PA [auth f] mmCIF format, chain MA [auth q] mmCIF format, chain IA [auth e] mmCIF format, chain DB [auth p]	DB [auth p] IA [auth e] MA [auth q] PA [auth f] WA [auth k] DB [auth p], IA [auth e], MA [auth q], PA [auth f], WA [auth k], XA [auth l]	iron-sulfur-molybdenum cluster with interstitial carbon C Fe₇ Mo S₉ DDQFAOMIVKLFON-UHFFFAOYSA-N		Interactions Focus chain DB [auth p] Focus chain IA [auth e] Focus chain MA [auth q] Focus chain PA [auth f] Focus chain WA [auth k] Focus chain XA [auth l] Interactions & Density Focus chain DB [auth p] Focus chain IA [auth e] Focus chain MA [auth q] Focus chain PA [auth f] Focus chain WA [auth k] Focus chain XA [auth l]
CLF (Subject of Investigation/LOI) Query on CLF Download:Ideal Coordinates CCD File SDF format, chain OA [auth f] SDF format, chain KA [auth q] SDF format, chain HA [auth e] SDF format, chain GA [auth W] SDF format, chain FA [auth N] SDF format, chain EA [auth M] MOL2 format, chain OA [auth f] MOL2 format, chain KA [auth q] MOL2 format, chain HA [auth e] MOL2 format, chain GA [auth W] MOL2 format, chain FA [auth N] MOL2 format, chain EA [auth M] mmCIF format, chain OA [auth f] mmCIF format, chain KA [auth q] mmCIF format, chain HA [auth e] mmCIF format, chain GA [auth W] mmCIF format, chain FA [auth N] mmCIF format, chain EA [auth M]	EA [auth M] FA [auth N] GA [auth W] HA [auth e] KA [auth q] EA [auth M], FA [auth N], GA [auth W], HA [auth e], KA [auth q], OA [auth f]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth W] Focus chain HA [auth e] Focus chain KA [auth q] Focus chain OA [auth f] Interactions & Density Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth W] Focus chain HA [auth e] Focus chain KA [auth q] Focus chain OA [auth f]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain ZA [auth m] SDF format, chain UA [auth j] SDF format, chain TA [auth i] SDF format, chain RA [auth g] SDF format, chain NA [auth a] SDF format, chain GB [auth t] SDF format, chain FB [auth s] SDF format, chain BB [auth o] SDF format, chain AB [auth n] MOL2 format, chain ZA [auth m] MOL2 format, chain UA [auth j] MOL2 format, chain TA [auth i] MOL2 format, chain RA [auth g] MOL2 format, chain NA [auth a] MOL2 format, chain GB [auth t] MOL2 format, chain FB [auth s] MOL2 format, chain BB [auth o] MOL2 format, chain AB [auth n] mmCIF format, chain ZA [auth m] mmCIF format, chain UA [auth j] mmCIF format, chain TA [auth i] mmCIF format, chain RA [auth g] mmCIF format, chain NA [auth a] mmCIF format, chain GB [auth t] mmCIF format, chain FB [auth s] mmCIF format, chain BB [auth o] mmCIF format, chain AB [auth n]	AB [auth n] BB [auth o] FB [auth s] GB [auth t] NA [auth a] AB [auth n], BB [auth o], FB [auth s], GB [auth t], NA [auth a], RA [auth g], TA [auth i], UA [auth j], ZA [auth m]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AB [auth n] Focus chain BB [auth o] Focus chain FB [auth s] Focus chain GB [auth t] Focus chain NA [auth a] Focus chain RA [auth g] Focus chain TA [auth i] Focus chain UA [auth j] Focus chain ZA [auth m] Interactions & Density Focus chain AB [auth n] Focus chain BB [auth o] Focus chain FB [auth s] Focus chain GB [auth t] Focus chain NA [auth a] Focus chain RA [auth g] Focus chain TA [auth i] Focus chain UA [auth j] Focus chain ZA [auth m]
HCA (Subject of Investigation/LOI) Query on HCA Download:Ideal Coordinates CCD File SDF format, chain YA [auth l] SDF format, chain VA [auth k] SDF format, chain QA [auth f] SDF format, chain LA [auth q] SDF format, chain JA [auth e] SDF format, chain CB [auth p] MOL2 format, chain YA [auth l] MOL2 format, chain VA [auth k] MOL2 format, chain QA [auth f] MOL2 format, chain LA [auth q] MOL2 format, chain JA [auth e] MOL2 format, chain CB [auth p] mmCIF format, chain YA [auth l] mmCIF format, chain VA [auth k] mmCIF format, chain QA [auth f] mmCIF format, chain LA [auth q] mmCIF format, chain JA [auth e] mmCIF format, chain CB [auth p]	CB [auth p] JA [auth e] LA [auth q] QA [auth f] VA [auth k] CB [auth p], JA [auth e], LA [auth q], QA [auth f], VA [auth k], YA [auth l]	3-HYDROXY-3-CARBOXY-ADIPIC ACID C₇ H₁₀ O₇ XKJVEVRQMLKSMO-SSDOTTSWSA-N		Interactions Focus chain CB [auth p] Focus chain JA [auth e] Focus chain LA [auth q] Focus chain QA [auth f] Focus chain VA [auth k] Focus chain YA [auth l] Interactions & Density Focus chain CB [auth p] Focus chain JA [auth e] Focus chain LA [auth q] Focus chain QA [auth f] Focus chain VA [auth k] Focus chain YA [auth l]
AKG (Subject of Investigation/LOI) Query on AKG Download:Ideal Coordinates CCD File SDF format, chain SA [auth h] SDF format, chain EB [auth r] MOL2 format, chain SA [auth h] MOL2 format, chain EB [auth r] mmCIF format, chain SA [auth h] mmCIF format, chain EB [auth r]	EB [auth r], SA [auth h]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain EB [auth r] Focus chain SA [auth h] Interactions & Density Focus chain EB [auth r] Focus chain SA [auth h]