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- PDB-9p1x: Cryo-EM structure of Nitrogenase MoFe protein from Methanosarcina... -

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Basic information

Entry
Database: PDB / ID: 9p1x
TitleCryo-EM structure of Nitrogenase MoFe protein from Methanosarcina acetivorans bound to the NifI inhibitor complex
Components
  • (P-II family nitrogen regulatory ...) x 2
  • Nitrogenase molybdenum-iron protein beta chain
  • Nitrogenase protein alpha chain
KeywordsOXIDOREDUCTASE / Metalloproteins / Nitrogenase / Methanogen / cryo-EM
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / regulation of nitrogen utilization / iron-sulfur cluster binding / enzyme regulator activity / DNA-templated transcription / ATP binding / metal ion binding / cytosol
Similarity search - Function
Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site ...Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2-OXOGLUTARIC ACID / FE(8)-S(7) CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase protein alpha chain / P-II family nitrogen regulatory protein / P-II family nitrogen regulatory protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsKashyap, R. / Antony, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020965 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Nitrogenase MoFe protein from Methanosarcina acetivorans bound to the NifI inhibitor complex
Authors: Kashyap, R. / Antony, E.
History
DepositionJun 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
K: Nitrogenase protein alpha chain
M: Nitrogenase molybdenum-iron protein beta chain
V: Nitrogenase protein alpha chain
W: Nitrogenase molybdenum-iron protein beta chain
X: Nitrogenase molybdenum-iron protein beta chain
H: P-II family nitrogen regulatory protein
J: P-II family nitrogen regulatory protein
R: P-II family nitrogen regulatory protein
T: P-II family nitrogen regulatory protein
b: P-II family nitrogen regulatory protein
d: P-II family nitrogen regulatory protein
L: Nitrogenase protein alpha chain
N: Nitrogenase molybdenum-iron protein beta chain
U: Nitrogenase protein alpha chain
G: P-II family nitrogen regulatory protein
E: P-II family nitrogen regulatory protein
F: P-II family nitrogen regulatory protein
I: P-II family nitrogen regulatory protein
Q: P-II family nitrogen regulatory protein
O: P-II family nitrogen regulatory protein
P: P-II family nitrogen regulatory protein
S: P-II family nitrogen regulatory protein
a: P-II family nitrogen regulatory protein
Y: P-II family nitrogen regulatory protein
Z: P-II family nitrogen regulatory protein
c: P-II family nitrogen regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)913,96458
Polymers900,54730
Non-polymers13,41828
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 12 molecules ACKVLUBDMWXN

#1: Protein
Nitrogenase protein alpha chain


Mass: 62884.285 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: A Methanosarcina acetivorans strain (DJL70) expressing an N-terminal twin-Strep-tagged NifD was engineered using CRISPR-Cas9. A gRNA targeting nifI2 was designed, and synthetic homology ...Details: A Methanosarcina acetivorans strain (DJL70) expressing an N-terminal twin-Strep-tagged NifD was engineered using CRISPR-Cas9. A gRNA targeting nifI2 was designed, and synthetic homology repair templates introduced the Strep-tag sequence upstream of nifD, along with a silent PAM mutation. The repair construct (pDL707) was assembled through Gibson assembly and Gateway cloning, transformed into M. acetivorans WWM73, and selected with puromycin and 8-ADP to remove the plasmid. PCR and sequencing confirmed successful integration of the Strep-tag at the nifD locus, yielding strain DJL70 which is a natural strain.
Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ90, nitrogenase
#2: Protein
Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase


Mass: 49478.605 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ89, nitrogenase

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P-II family nitrogen regulatory ... , 2 types, 18 molecules HJRTbdFIPSZcGEQOaY

#3: Protein
P-II family nitrogen regulatory protein


Mass: 11873.998 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ92
#4: Protein
P-II family nitrogen regulatory protein


Mass: 13980.253 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: nifI2, MA_3897 / Production host: Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ91

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Non-polymers , 5 types, 28 molecules

#5: Chemical
ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimeric complex of MoFe protein bound to NifI inhibitor complex
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.7.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74083 / Symmetry type: POINT
RefinementHighest resolution: 3.16 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00361216
ELECTRON MICROSCOPYf_angle_d0.5382551
ELECTRON MICROSCOPYf_dihedral_angle_d6.3078530
ELECTRON MICROSCOPYf_chiral_restr0.0449234
ELECTRON MICROSCOPYf_plane_restr0.00410669

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