8AHX

Cryo-EM structure of the nitrogen-fixation associated NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii

PDB DOI: https://doi.org/10.2210/pdb8AHX/pdb
EM Map EMD-15452: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Azotobacter vinelandii DJ
Expression System: Azotobacter vinelandii DJ
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2022-07-24 Released: 2023-11-01
Deposition Author(s): Zhang, L., Einsle, O.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.11 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Architecture of the NADH:ferredoxin oxidoreductase RNF that drives Biological Nitrogen Fixation

Zhang, L., Einsle, O.

To be published.

Macromolecule Content

Total Structure Weight: 201.21 kDa
Atom Count: 12,687
Modelled Residue Count: 1,608
Deposited Residue Count: 1,787
Unique protein chains: 7

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion-translocating oxidoreductase complex subunit A	A	190	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfA1, rnfA, Avin_50980 EC: 7 Membrane Entity: Yes
UniProt
Find proteins for C1DMA8 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMA8 Go to UniProtKB: C1DMA8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DMA8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion-translocating oxidoreductase complex subunit B	B	174	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfB1, rnfB, Avin_50970 EC: 7 Membrane Entity: Yes
UniProt
Find proteins for C1DMA7 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMA7 Go to UniProtKB: C1DMA7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DMA7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion-translocating oxidoreductase complex subunit C	C	496	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfC1, rnfC, Avin_50960 EC: 7 Membrane Entity: Yes
UniProt
Find proteins for C1DMA6 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMA6 Go to UniProtKB: C1DMA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DMA6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion-translocating oxidoreductase complex subunit D	D	366	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfD1, rnfD, Avin_50950 EC: 7 Membrane Entity: Yes
UniProt
Find proteins for C1DMA5 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMA5 Go to UniProtKB: C1DMA5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DMA5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion-translocating oxidoreductase complex subunit E	E	238	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfE, Avin_50930 EC: 7 Membrane Entity: Yes
UniProt
Find proteins for Q9F5Y1 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore Q9F5Y1 Go to UniProtKB: Q9F5Y1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9F5Y1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion-translocating oxidoreductase complex subunit G	F [auth G]	237	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfG1, rnfG, Avin_50940 EC: 7 Membrane Entity: Yes
UniProt
Find proteins for C1DMA4 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMA4 Go to UniProtKB: C1DMA4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DMA4
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein RnfH	G [auth H]	86	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: rnfH, Avin_50920
UniProt
Find proteins for Q9F5Y0 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore Q9F5Y0 Go to UniProtKB: Q9F5Y0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9F5Y0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] I [auth A] AA [auth E], BA [auth E], CA [auth E], DA [auth E], I [auth A], J [auth A], P [auth D], Q [auth D], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain EA [auth G] SDF format, chain M [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain EA [auth G] MOL2 format, chain M [auth C]	EA [auth G], M [auth C], Z [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain EA [auth G] Focus chain M [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth G] Focus chain M [auth C] Focus chain Z [auth D]
RBF (Subject of Investigation/LOI) Query on RBF Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D]	R [auth D]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	K [auth B], L [auth B], N [auth C], O [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.11 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Zhang, L.

Einsle, O.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	310656
German Research Foundation (DFG)	Germany	CRC 1381, project ID 403222702
German Research Foundation (DFG)	Germany	RTG 2202, project ID 46710898
German Research Foundation (DFG)	Germany	grant INST 35/134-1 FUGG

Revision History (Full details and data files)

Version 1.0: 2023-11-01
Type: Initial release

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Help and Resources

8AHX

Cryo-EM structure of the nitrogen-fixation associated NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii

Architecture of the NADH:ferredoxin oxidoreductase RNF that drives Biological Nitrogen Fixation

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Experimental Data

Structure Validation

Deposition Data

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