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- EMDB-48907: Decameric Glucose-6-phosphate isomerase from Azotobacter vinelandii -

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Basic information

Entry
Database: EMDB / ID: EMD-48907
TitleDecameric Glucose-6-phosphate isomerase from Azotobacter vinelandii
Map data
Sample
  • Complex: Decameric complex of Glucose-6-phosphate isomerase
    • Protein or peptide: Glucose-6-phosphate isomerase
KeywordsGlycolysis / decamer / ISOMERASE
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWarmack RA / Maggiolo AO
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
DepositionFeb 3, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48907.png

Downloads & links

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Map

FileDownload / File: emd_48907.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.9589287 - 1.6656667
Average (Standard dev.)-0.0000958147 (±0.037124895)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_48907_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48907_half_map_2.map
Projections & Slices
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Sample components

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Entire : Decameric complex of Glucose-6-phosphate isomerase

EntireName: Decameric complex of Glucose-6-phosphate isomerase
Components
  • Complex: Decameric complex of Glucose-6-phosphate isomerase
    • Protein or peptide: Glucose-6-phosphate isomerase

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Supramolecule #1: Decameric complex of Glucose-6-phosphate isomerase

SupramoleculeName: Decameric complex of Glucose-6-phosphate isomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

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Macromolecule #1: Glucose-6-phosphate isomerase

MacromoleculeName: Glucose-6-phosphate isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: glucose-6-phosphate isomerase
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 61.978125 KDa
SequenceString: MSYYQQAFDV TSLPSWRALQ EHRLAMQNFH MREAFLSDPG RFDEFSTSSC GLFLDYSKNL ITPETRDLLV NLAREAGVEQ AARAMFDGE PVNASERRPA LHTALRRPVG DSLLIDGHNI MRDVHAALAQ MTDIVGRIHN KLWRGYSDRA ITDVVNIGIG G SYLGPELV ...String:
MSYYQQAFDV TSLPSWRALQ EHRLAMQNFH MREAFLSDPG RFDEFSTSSC GLFLDYSKNL ITPETRDLLV NLAREAGVEQ AARAMFDGE PVNASERRPA LHTALRRPVG DSLLIDGHNI MRDVHAALAQ MTDIVGRIHN KLWRGYSDRA ITDVVNIGIG G SYLGPELV SEALLPYTQH GVRCHYLANI DGSEFHELTA RLNAETTLFI ISSKTFGTLE TLKNAQAART WYLASGGSEE RL YRHFIAV TSNIPAAIEF GIREKNIFPM WDWVGGRYSL WSAIGLPTAL AIGMANFKDL LSGAYAMDCH FRREPFENNM PVL LAMLGV WYGNFWGAQS HAILPYDHYL RNFVKHLQQM DMESNGKSVR QDGSPVSCET GPVIWGGVGC NGQHAYHQLL HQGT LLIPA DFIVPVVSHN PVADHHQWLY ANCLSQSQAL MLGKSREEAE AELRAKGLPE AEVKRLAPHK VIPGNRPSNT LVMET LNPS RLGALIALYE HKVFVQGVIW GINSFDQWGV ELGKELGKNV YGRLTSYEAP PAEDSSTQGL IDYFRGRHRG

UniProtKB: Glucose-6-phosphate isomerase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70453
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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