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- PDB-8ahx: Cryo-EM structure of the nitrogen-fixation associated NADH:ferred... -

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Basic information

Entry
Database: PDB / ID: 8ahx
TitleCryo-EM structure of the nitrogen-fixation associated NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii
Components
  • (Ion-translocating oxidoreductase complex subunit ...) x 6
  • Protein RnfH
KeywordsMEMBRANE PROTEIN / metalloprotein / flavoprotein / electron transfer and Na+/H+ translocation
Function / homology
Function and homology information


Translocases / prenyltransferase activity / metabolic process / electron transport chain / transmembrane transport / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Ion-translocating oxidoreductase complex, RnfB/RsxB / Ion-translocating oxidoreductase complex subunit E / Ion-translocating oxidoreductase complex, subunit RnfA/RsxA / Ion-translocating oxidoreductase complex Rnf, subunit D / Electron transport complex, RnfB/RsxB, Proteobacteria / RnfH protein / Ion-translocating oxidoreductase complex, subunit RnfG/RsxG / RnfH superfamily / RnfH family Ubiquitin / 4Fe-4S domain ...Ion-translocating oxidoreductase complex, RnfB/RsxB / Ion-translocating oxidoreductase complex subunit E / Ion-translocating oxidoreductase complex, subunit RnfA/RsxA / Ion-translocating oxidoreductase complex Rnf, subunit D / Electron transport complex, RnfB/RsxB, Proteobacteria / RnfH protein / Ion-translocating oxidoreductase complex, subunit RnfG/RsxG / RnfH superfamily / RnfH family Ubiquitin / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / Aromatic prenyltransferase Orf2 / FMN-binding / FMN-binding domain / FMN_bind / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / 4Fe-4S dicluster domain / Aromatic prenyltransferase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN / IRON/SULFUR CLUSTER / Ion-translocating oxidoreductase complex subunit G / Ion-translocating oxidoreductase complex subunit D / Prenyltransferase / Ion-translocating oxidoreductase complex subunit B / Ion-translocating oxidoreductase complex subunit A / Protein RnfH / Ion-translocating oxidoreductase complex subunit E
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang, L. / Einsle, O.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Research Council (ERC)310656European Union
German Research Foundation (DFG)CRC 1381, project ID 403222702 Germany
German Research Foundation (DFG)RTG 2202, project ID 46710898 Germany
German Research Foundation (DFG)grant INST 35/134-1 FUGG Germany
CitationJournal: To Be Published
Title: Architecture of the NADH:ferredoxin oxidoreductase RNF that drives Biological Nitrogen Fixation
Authors: Zhang, L. / Einsle, O.
History
DepositionJul 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion-translocating oxidoreductase complex subunit A
B: Ion-translocating oxidoreductase complex subunit B
C: Ion-translocating oxidoreductase complex subunit C
D: Ion-translocating oxidoreductase complex subunit D
E: Ion-translocating oxidoreductase complex subunit E
G: Ion-translocating oxidoreductase complex subunit G
H: Protein RnfH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,21131
Polymers190,2247
Non-polymers10,98724
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35690 Å2
ΔGint-277 kcal/mol
Surface area67170 Å2
MethodPISA

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Components

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Ion-translocating oxidoreductase complex subunit ... , 6 types, 6 molecules ABCDEG

#1: Protein Ion-translocating oxidoreductase complex subunit A / Rnf electron transport complex subunit A


Mass: 19942.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfA1, rnfA, Avin_50980 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DMA8, Translocases
#2: Protein Ion-translocating oxidoreductase complex subunit B / Rnf electron transport complex subunit B


Mass: 17704.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfB1, rnfB, Avin_50970 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DMA7, Translocases
#3: Protein Ion-translocating oxidoreductase complex subunit C / Rnf electron transport complex subunit C


Mass: 52234.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfC1, rnfC, Avin_50960 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DMA6, Translocases
#4: Protein Ion-translocating oxidoreductase complex subunit D / Rnf electron transport complex subunit D


Mass: 39189.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfD1, rnfD, Avin_50950 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DMA5, Translocases
#5: Protein Ion-translocating oxidoreductase complex subunit E / Rnf electron transport complex subunit E


Mass: 25576.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfE, Avin_50930 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: Q9F5Y1, Translocases
#6: Protein Ion-translocating oxidoreductase complex subunit G / Rnf electron transport complex subunit G


Mass: 25932.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfG1, rnfG, Avin_50940 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DMA4, Translocases

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Protein / Sugars , 2 types, 16 molecules H

#7: Protein Protein RnfH


Mass: 9644.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: rnfH, Avin_50920 / Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: Q9F5Y0
#9: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 9 molecules

#8: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#10: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#11: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Heptameric complex of NADH:ferredoxin oxidoreductase RNF
Type: COMPLEX / Entity ID: #1-#3, #5, #7 / Source: NATURAL
Molecular weightValue: 0.188 MDa / Experimental value: NO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94807 / Symmetry type: POINT

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