[English] 日本語
Yorodumi
- EMDB-49753: CryoEM structure of ancestral nitrogenase MoFe-protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49753
TitleCryoEM structure of ancestral nitrogenase MoFe-protein
Map data
Sample
  • Complex: Nitrogenase MoFe-protein
    • Protein or peptide: Nitrogenase MoFe-protein alpha chain
    • Protein or peptide: Nitrogenase MoFe-protein beta chain
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsMetalloprotein / OXIDOREDUCTASE
Biological speciesAzotobacter vinelandii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsShen Y / Warmack RA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: Structure / Year: 2025
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.
Authors: Yuanbo Shen / Ailiena O Maggiolo / Tianzheng Zhang / Rebeccah A Warmack /
Abstract: Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry ...Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.
History
DepositionMar 17, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49753.png

Downloads & links

-
Map

FileDownload / File: emd_49753.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.595
Minimum - Maximum-2.1293294 - 3.4486768
Average (Standard dev.)-0.000021175543 (±0.057623442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_49753_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49753_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nitrogenase MoFe-protein

EntireName: Nitrogenase MoFe-protein
Components
  • Complex: Nitrogenase MoFe-protein
    • Protein or peptide: Nitrogenase MoFe-protein alpha chain
    • Protein or peptide: Nitrogenase MoFe-protein beta chain
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: FE (III) ION
  • Ligand: water

-
Supramolecule #1: Nitrogenase MoFe-protein

SupramoleculeName: Nitrogenase MoFe-protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

-
Macromolecule #1: Nitrogenase MoFe-protein alpha chain

MacromoleculeName: Nitrogenase MoFe-protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 55.73318 KDa
SequenceString: MTGMSRDEVE SLIQEVLEVY PEKAKKNREK HLSPNDPELE QSKKCITSNK KSLPGVMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEIE TLFPLNKGIS VQSECPIGLI G DDIEAVSK ...String:
MTGMSRDEVE SLIQEVLEVY PEKAKKNREK HLSPNDPELE QSKKCITSNK KSLPGVMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCG QYSRAGRRNY YIGTTGVNAF VTMNFTSDFQ EKDIVFGGDK KLAKLIDEIE TLFPLNKGIS VQSECPIGLI G DDIEAVSK QKGKEHGKTI VPVRCEGFRG VSQSLGHHIA NDAVRDWVLS ARDDDDSFET TDYDVAIIGD YNIGGDAWSS RI LLEEMGL RVVAQWSGDG TISEMELTPK VKLNLVHCYR SMNYISRHME EKYGIPWMEY NFFGPTKTIE SLRKIAAQFD ESI QKKCEE VIAKYQPEWE AVVAKYRPRL EGKRVMLYVG GLRPRHVIGA YEDLGMEVVG TGYEFGHNDD YDRTLKEMGD STLL YDDVT GYEFEEFVKK VKPDLIGSGI KEKYIFQKMG IPFRQMHSWD YSGPYHGFDG FAIFARDMDM TLNNPCWKKL QAPWK KSEQ ADEAVAASA

-
Macromolecule #2: Nitrogenase MoFe-protein beta chain

MacromoleculeName: Nitrogenase MoFe-protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 60.071207 KDa
SequenceString: MSQQVDNIKP SYPLFRDQDY KDMLAKKRDN FEEKHPQEKI DEVFQWTTTE EYQELNFQRE ALTVNPAKAC QPLGAVLCSL GFEKTMPYV HGSQGCVAYF RTYFNRHFKE PISCVSDSMT EDAAVFGGQQ NMKDGLQNCK AIYKPDMIAV STTCMAEVIG D DLNAFINN ...String:
MSQQVDNIKP SYPLFRDQDY KDMLAKKRDN FEEKHPQEKI DEVFQWTTTE EYQELNFQRE ALTVNPAKAC QPLGAVLCSL GFEKTMPYV HGSQGCVAYF RTYFNRHFKE PISCVSDSMT EDAAVFGGQQ NMKDGLQNCK AIYKPDMIAV STTCMAEVIG D DLNAFINN SKKEGHIPDE FPVPFAHTPS FVGSHVTGWD NMFEGIARYF TLNYMEDKEV GSNGKINIVP GFETYLGNFR VI KRMMNEM NVDYTLLSDP EEVLDTPADG QFRMYAGGTT QDEMKDAPNA LNTLMLQPWQ LTKTTKFVKN TWKHEVPKLN IPM GLDWTD EFLMKVSEIS GQPIPESLAK ERGRLVDMMT DSHTWLHGKK FALWGDPDFV MGMTKFLLEL GCEPIHILCN NANK RWKKA MDAILAESPY GANSEVHIGK DLWHMRSLVF TNKPDFMIGN SYGKFIQRDT LYKGKEFEVP LIRIGFPIFD RHHLH RQTT LGYEGAMQIL TTLVNSVLER LDEETRGMQT TDYNYDLVR

-
Macromolecule #3: iron-sulfur-molybdenum cluster with interstitial carbon

MacromoleculeName: iron-sulfur-molybdenum cluster with interstitial carbon
type: ligand / ID: 3 / Number of copies: 2 / Formula: ICS
Molecular weightTheoretical: 787.451 Da
Chemical component information

ChemComp-ICE:
iron-sulfur-molybdenum cluster with interstitial carbon

-
Macromolecule #4: 3-HYDROXY-3-CARBOXY-ADIPIC ACID

MacromoleculeName: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: HCA
Molecular weightTheoretical: 206.15 Da
Chemical component information

ChemComp-HCA:
3-HYDROXY-3-CARBOXY-ADIPIC ACID

-
Macromolecule #5: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

ChemComp-CLF:
FE(8)-S(7) CLUSTER

-
Macromolecule #6: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1394 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192110
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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