[English] 日本語
Yorodumi
- EMDB-15452: Cryo-EM structure of the nitrogen-fixation associated NADH:ferred... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15452
TitleCryo-EM structure of the nitrogen-fixation associated NADH:ferredoxin oxidoreductase RNF from Azotobacter vinelandii
Map dataunsharpened map
Sample
  • Complex: Heptameric complex of NADH:ferredoxin oxidoreductase RNF
    • Protein or peptide: x 5 types
  • Protein or peptide: x 2 types
  • Ligand: x 5 types
Keywordsmetalloprotein / flavoprotein / electron transfer and Na+/H+ translocation / MEMBRANE PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang L / Einsle O
Funding supportEuropean Union, Germany, 4 items
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, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15452.png

Downloads & links

-
Map

FileDownload / File: emd_15452.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 280 pix.
= 229.6 Å		0.82 Å/pix.
x 280 pix.
= 229.6 Å		0.82 Å/pix.
x 280 pix.
= 229.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.19443077 - 0.9367607
Average (Standard dev.)0.0019276759 (±0.02037143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 229.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharpened map

Fileemd_15452_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halp map A

Fileemd_15452_half_map_1.map
Annotationhalp map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halp map B

Fileemd_15452_half_map_2.map
Annotationhalp map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Heptameric complex of NADH:ferredoxin oxidoreductase RNF

EntireName: Heptameric complex of NADH:ferredoxin oxidoreductase RNF
Components
  • Complex: Heptameric complex of NADH:ferredoxin oxidoreductase RNF
    • Protein or peptide: Ion-translocating oxidoreductase complex subunit A
    • Protein or peptide: Ion-translocating oxidoreductase complex subunit B
    • Protein or peptide: Ion-translocating oxidoreductase complex subunit C
    • Protein or peptide: Ion-translocating oxidoreductase complex subunit E
    • Protein or peptide: Protein RnfH
  • Protein or peptide: Ion-translocating oxidoreductase complex subunit D
  • Protein or peptide: Ion-translocating oxidoreductase complex subunit G
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: RIBOFLAVIN

+
Supramolecule #1: Heptameric complex of NADH:ferredoxin oxidoreductase RNF

SupramoleculeName: Heptameric complex of NADH:ferredoxin oxidoreductase RNF
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5, #7
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 188 KDa

+
Macromolecule #1: Ion-translocating oxidoreductase complex subunit A

MacromoleculeName: Ion-translocating oxidoreductase complex subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 19.942131 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString:
MEYVLFLLGT VLVHNVVLVG FLGLCPFMGV SSKLDPSIGL AVATTLVMGL GGASSWLLEH YVLLPLGIGF IRILAYIVVI AGMVQLIEM IIRKASPSLY RSLGIYLPLI TTNCAVLGVP LLSVREGHDL TMAVLFGLGS GLGFSLIMII FAGLRERLAL A NVPAAFSG PPIAFVTAGL LALAFMGFGG LI

UniProtKB: Ion-translocating oxidoreductase complex subunit A

+
Macromolecule #2: Ion-translocating oxidoreductase complex subunit B

MacromoleculeName: Ion-translocating oxidoreductase complex subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 17.704572 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString:
MIEATLALTV MGVLLGCGLG LAARKFAVTD ENPLIKEVSD LMPGSQCGQC GFPGCGAAAV AIVEGNASVT CCPPGGVGLA EKLAAILGV PLDASQVAAP MLARVEASQC IGCTRCYRAC PTDAIVGASG QVHVVLEDAC TGCGKCRDAC PEDCVLLIPQ E QTLDTWRW DKPAAA

UniProtKB: Ion-translocating oxidoreductase complex subunit B

+
Macromolecule #3: Ion-translocating oxidoreductase complex subunit C

MacromoleculeName: Ion-translocating oxidoreductase complex subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 52.234195 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MYFNLSSIRG GVHPAAHKDL SAALPIGSLP LPPRLYLPLR QHAGAEALPM VAVGDKVLKG QLLAFPPTEV SAPVHAPTSG RIVAIGPVP APHPSGLTTT GIVLESDGED RWIDLDVSTD PFAEDPLVLA DRVAKAGIVG LGGAIFPAAV KLKQGTRHEI K TVLVNGSE ...String:
MYFNLSSIRG GVHPAAHKDL SAALPIGSLP LPPRLYLPLR QHAGAEALPM VAVGDKVLKG QLLAFPPTEV SAPVHAPTSG RIVAIGPVP APHPSGLTTT GIVLESDGED RWIDLDVSTD PFAEDPLVLA DRVAKAGIVG LGGAIFPAAV KLKQGTRHEI K TVLVNGSE CEPYLTCDDR IMRERAEAIV DGARLIQHIL RAYSVVIAIE DNKPEALAAM RAAAEHFGAI EVMAVPALYP MG SAKQLIQ AVTGREVPAG GRSTDVGVLV HNAGTVYAIQ QALRFGRPLI SRVVTVSGAC VKTPQNLDVL IGTPVQALID ACG GLSGDP QQLLLGGPMM GAVLPSTEVP VIKGATGLLA LARHELPNKD PAPCIRCASC VDACPMGLTP LDMALYARAD DYDG ASEYG LRDCILCGCC SYVCPSHIPL VHYFQYAKGQ QDERRSAARK SDYIKRQTEV RAARLAEEEA AKAAAKAAKE AAKAA KAAK TKAAKPSNEV ES

UniProtKB: Prenyltransferase

+
Macromolecule #4: Ion-translocating oxidoreductase complex subunit D

MacromoleculeName: Ion-translocating oxidoreductase complex subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 39.189016 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MSTISVAAGP FAHDRSSVNR IMLDVCLALT PATLFGLVMF GWPAINLWLV TCVSALAIEA ACLRLLGQPM RRLLDGSALL TGWLLAISL PPWAPWWIGV GGSLFAIGIG KQLYGGIGQN PFNPAMLARV ALLIAFPLQM TTWALPHPLF SSSAPGFFDS L AITFAGAP ...String:
MSTISVAAGP FAHDRSSVNR IMLDVCLALT PATLFGLVMF GWPAINLWLV TCVSALAIEA ACLRLLGQPM RRLLDGSALL TGWLLAISL PPWAPWWIGV GGSLFAIGIG KQLYGGIGQN PFNPAMLARV ALLIAFPLQM TTWALPHPLF SSSAPGFFDS L AITFAGAP LADGMTGATA LGNLKTELTL NRTAQEILEG GFSTISALFG STPGSLGETS ELLLLVGGVW LVLRRIIHWE IP VAILASV FVMATLAYLI NPERYAGGLY QLTSGGLILC AFFIATDPVT SPISRVGRLI FGVGCGVLIY VIRTWGSFPE AAA FAVLFM NALTPLIDRY WRPRAYGRNV RGKPLVAAKW TSQVKEVDKV

UniProtKB: Ion-translocating oxidoreductase complex subunit D

+
Macromolecule #5: Ion-translocating oxidoreductase complex subunit E

MacromoleculeName: Ion-translocating oxidoreductase complex subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 25.576328 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MSHCGAPSVP EPEKKVPWQY FTSALWQYNV ALVQMLALCP TLAVTTTATN GLGMGLATTL VLVMTNALIS SMRHTISPEV RNPVMIGVI AGVVTLTDMA MNAWMHELYK VLGLFIALIV TNCAVLGRAE SFCLRNPVIP SILDGAGMGA GFTAVLVVIG G IREILGSG ...String:
MSHCGAPSVP EPEKKVPWQY FTSALWQYNV ALVQMLALCP TLAVTTTATN GLGMGLATTL VLVMTNALIS SMRHTISPEV RNPVMIGVI AGVVTLTDMA MNAWMHELYK VLGLFIALIV TNCAVLGRAE SFCLRNPVIP SILDGAGMGA GFTAVLVVIG G IREILGSG TLFSQASSLL GSHFKWMEIT VIPDFQGILL AILPPGAFIV LGFLLAAKRV IDRKRAERRQ QTHGELVVLQ

UniProtKB: Ion-translocating oxidoreductase complex subunit E

+
Macromolecule #6: Ion-translocating oxidoreductase complex subunit G

MacromoleculeName: Ion-translocating oxidoreductase complex subunit G / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 25.932709 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString: MNDTTMTPAE ENAAPAEAAA GKPTLLARLE KWRPMVAYQG LSLGLVCAVV ALLLLTGNIM THGTIAEQQM QDRLATLREV LPQSLYDNN PLADSFKVQD AELGEVEVLP ARLQGKLTAV VFQGRNIGYG GPIEQMMSVD AQGKILGVRV LTHKETPGLA D KIEASRSD ...String:
MNDTTMTPAE ENAAPAEAAA GKPTLLARLE KWRPMVAYQG LSLGLVCAVV ALLLLTGNIM THGTIAEQQM QDRLATLREV LPQSLYDNN PLADSFKVQD AELGEVEVLP ARLQGKLTAV VFQGRNIGYG GPIEQMMSVD AQGKILGVRV LTHKETPGLA D KIEASRSD WIKVFDGLSL ENTALDKWKV KKDGGQFDQF AGATITPRAV VKTVLQGLQF QARHAEQLKA EWSHPQFEK

UniProtKB: Ion-translocating oxidoreductase complex subunit G

+
Macromolecule #7: Protein RnfH

MacromoleculeName: Protein RnfH / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 9.644859 KDa
Recombinant expressionOrganism: Azotobacter vinelandii DJ (bacteria)
SequenceString:
MRVSVVYADP AKPLQLSCKV EDGCSVEQAI QQSGVLRCCP DIDLKKQKVG VFGKFVKLDS PLKDGDRIEI YQRVTRVDDD DDDDDD

UniProtKB: Protein RnfH

+
Macromolecule #8: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

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

+
Macromolecule #9: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 9 / Number of copies: 15 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

+
Macromolecule #11: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 11 / Number of copies: 3 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

+
Macromolecule #12: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 12 / Number of copies: 1 / Formula: RBF
Molecular weightTheoretical: 376.364 Da
Chemical component information

ChemComp-RBF:
RIBOFLAVIN / Riboflavin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94807

+
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