[English] 日本語
Yorodumi
- PDB-8rho: [2Fe:2S] ferredoxin FeSII from Azotobacter vinelandii, reduced form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rho
Title[2Fe:2S] ferredoxin FeSII from Azotobacter vinelandii, reduced form
ComponentsFerredoxin
KeywordsMETAL BINDING PROTEIN / [2Fe:2S] ferredoxin FeSII
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding
Similarity search - Function
2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / Ferredoxin
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFranke, P. / Zhang, L. / Einsle, O.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
European Research Council (ERC)310656European Union
German Research Foundation (DFG)RTG 1976, project ID 235777276 Germany
German Research Foundation (DFG)CRC 1381, project ID 403222702 Germany
CitationJournal: Nature / Year: 2025
Title: Conformational protection of molybdenum nitrogenase by Shethna protein II.
Authors: Philipp Franke / Simon Freiberger / Lin Zhang / Oliver Einsle /
Abstract: The oxygen-sensitive molybdenum-dependent nitrogenase of Azotobacter vinelandii is protected from oxidative damage by a reversible 'switch-off' mechanism. It forms a complex with a small ferredoxin, ...The oxygen-sensitive molybdenum-dependent nitrogenase of Azotobacter vinelandii is protected from oxidative damage by a reversible 'switch-off' mechanism. It forms a complex with a small ferredoxin, FeSII (ref. ) or the 'Shethna protein II', which acts as an O sensor and associates with the two component proteins of nitrogenase when its [2Fe:2S] cluster becomes oxidized. Here we report the three-dimensional structure of the protective ternary complex of the catalytic subunit of Mo-nitrogenase, its cognate reductase and the FeSII protein, determined by single-particle cryo-electron microscopy. The dimeric FeSII protein associates with two copies of each component to assemble a 620 kDa core complex that then polymerizes into large, filamentous structures. This complex is catalytically inactive, but the enzyme components are quickly released and reactivated upon oxygen depletion. The first step in complex formation is the association of FeSII with the more O-sensitive Fe protein component of nitrogenase during sudden oxidative stress. The action of this small ferredoxin represents a straightforward means of protection from O that may be crucial for the maintenance of recombinant nitrogenase in food crops.
History
DepositionDec 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferredoxin
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,73512
Polymers26,5792
Non-polymers1,15710
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-13 kcal/mol
Surface area11500 Å2
Unit cell
Length a, b, c (Å)60.955, 60.955, 139.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ferredoxin


Mass: 13289.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: Avin_39700 / Production host: Escherichia coli (E. coli) / Variant (production host): C43(DE3) / References: UniProt: C1DE01

-
Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 50 mM glycine at pH 9 and 55 % (v/v) PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→46.47 Å / Num. obs: 88800 / % possible obs: 100 % / Redundancy: 23.1 % / CC1/2: 1 / Net I/σ(I): 28.5
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 2280 / CC1/2: 0.809

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→27.1 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1816 4338 4.89 %
Rwork0.1523 --
obs0.1537 88800 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 61 262 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.471
X-RAY DIFFRACTIONf_dihedral_angle_d9.558293
X-RAY DIFFRACTIONf_chiral_restr0.079299
X-RAY DIFFRACTIONf_plane_restr0.012341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.35281420.3012792X-RAY DIFFRACTION100
1.47-1.480.33421560.28162804X-RAY DIFFRACTION100
1.48-1.50.29441400.25822801X-RAY DIFFRACTION100
1.5-1.520.27791490.2562822X-RAY DIFFRACTION100
1.52-1.540.28581190.24512827X-RAY DIFFRACTION100
1.54-1.560.2181480.2182834X-RAY DIFFRACTION100
1.56-1.580.26981220.20152848X-RAY DIFFRACTION100
1.58-1.610.21361740.2052764X-RAY DIFFRACTION100
1.61-1.630.21341480.19022800X-RAY DIFFRACTION100
1.63-1.660.2371630.18392824X-RAY DIFFRACTION100
1.66-1.690.23651440.17552813X-RAY DIFFRACTION100
1.69-1.720.18661480.16722782X-RAY DIFFRACTION100
1.72-1.750.19661460.1542800X-RAY DIFFRACTION100
1.75-1.790.20351430.15652844X-RAY DIFFRACTION100
1.79-1.830.20871520.15262773X-RAY DIFFRACTION100
1.83-1.870.21351550.15782808X-RAY DIFFRACTION100
1.87-1.920.20341640.13442835X-RAY DIFFRACTION100
1.92-1.970.1591580.13522808X-RAY DIFFRACTION100
1.97-2.030.15281090.13312825X-RAY DIFFRACTION100
2.03-2.090.16551590.1372812X-RAY DIFFRACTION100
2.09-2.170.18291560.13162817X-RAY DIFFRACTION100
2.17-2.250.19561240.13452826X-RAY DIFFRACTION100
2.25-2.350.19791580.14262819X-RAY DIFFRACTION100
2.35-2.480.16161240.14212821X-RAY DIFFRACTION100
2.48-2.630.24641420.14832843X-RAY DIFFRACTION100
2.63-2.840.1971340.14272817X-RAY DIFFRACTION100
2.84-3.120.16591140.14632845X-RAY DIFFRACTION100
3.12-3.570.1671280.13822857X-RAY DIFFRACTION100
3.57-4.50.14311400.13792820X-RAY DIFFRACTION100
4.5-27.10.16811790.17032781X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more