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- EMDB-49800: CryoEM analysis of Phosphoglucose isomerase from P. aeruginosa re... -

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Basic information

Entry
Database: EMDB / ID: EMD-49800
TitleCryoEM analysis of Phosphoglucose isomerase from P. aeruginosa reveals potential clinically relevant features
Map dataSharpened Map for Model Building
Sample
  • Organelle or cellular component: Oligomeric structure of PGI
    • Protein or peptide: Glucose-6-phosphate isomerase
  • Ligand: 6-PHOSPHOGLUCONIC ACID
  • Ligand: water
KeywordsPhosphoglucose Isomerase / STRUCTURAL PROTEIN
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 speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.45 Å
AuthorsSharma K / Borgnia JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: To Be Published
Title: CryoEM analysis of Phosphoglucose isomerase from P. aeruginosa reveals potential clinically relevant features
Authors: Sharma K / Borgnia JM
History
DepositionMar 19, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49800.png

Downloads & links

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Map

FileDownload / File: emd_49800.map.gz / Format: CCP4 / Size: 55.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map for Model Building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.68 Å/pix.
x 301 pix.
= 203.175 Å		0.68 Å/pix.
x 289 pix.
= 195.075 Å		0.68 Å/pix.
x 167 pix.
= 112.725 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.455
Minimum - Maximum-5.362671 - 17.54843
Average (Standard dev.)0.000000000006903 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin179236170
Dimensions289167301
Spacing301289167
CellA: 203.175 Å / B: 195.075 Å / C: 112.725 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49800_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened Map

Fileemd_49800_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49800_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49800_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Oligomeric structure of PGI

EntireName: Oligomeric structure of PGI
Components
  • Organelle or cellular component: Oligomeric structure of PGI
    • Protein or peptide: Glucose-6-phosphate isomerase
  • Ligand: 6-PHOSPHOGLUCONIC ACID
  • Ligand: water

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Supramolecule #1: Oligomeric structure of PGI

SupramoleculeName: Oligomeric structure of PGI / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Location in cell: cytoplasm
Molecular weightTheoretical: 650 KDa

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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: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 62.275504 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GSMKHHLTPL DATQLDSWRA LAAHRQELQD FRMRQAFIDD PERFKRFSFS ACGLFLDFSK NLIRQDTIDL LVKLAEEARL SDAIRAMFD GEAINASERR PVLHTALRRP IGDKVLVDGV DVMPEVHRVL HQMTELVGYV HNGLWRGYTE KPITDVVNIG I GGSFLGPQ ...String:
GSMKHHLTPL DATQLDSWRA LAAHRQELQD FRMRQAFIDD PERFKRFSFS ACGLFLDFSK NLIRQDTIDL LVKLAEEARL SDAIRAMFD GEAINASERR PVLHTALRRP IGDKVLVDGV DVMPEVHRVL HQMTELVGYV HNGLWRGYTE KPITDVVNIG I GGSFLGPQ LVSEALLPFA QKGVRCHYLA NIDGSEFHEL ASRLNAETTL FIVSSKSFGT LETLKNAQAA RAWYLAQGGT EE ELYRHFI AVSSNKEAAI AFGIREENIF PMWDWVGGRY SLWSAIGLPI AMSIGISNFK ELLSGAYNMD QHFQTAPFER NIP VLLGLL GVWYGDFWGA NSHAILPYDY YLRNITDHLQ QLDMESNGKS VRQDGTPVTS GTGPVIWGGV GCNGQHAYHQ LLHQ GTQLI PADFIVPVSS YNPVADHHQW LYANCLSQSQ ALMLGKSREE AEAELRAKGL PEAEVQRLAP HKVIPGNRPS NTLVV ERIS ARRLGALIAM YEHKVYVQSI LWGINAFDQW GVELGKELGK GVYSRLVGSE ETPAEDASTQ GLIDFFRGRH RGL

UniProtKB: Glucose-6-phosphate isomerase

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Macromolecule #2: 6-PHOSPHOGLUCONIC ACID

MacromoleculeName: 6-PHOSPHOGLUCONIC ACID / type: ligand / ID: 2 / Number of copies: 10 / Formula: 6PG
Molecular weightTheoretical: 276.135 Da
Chemical component information

ChemComp-6PG:
6-PHOSPHOGLUCONIC ACID

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 6750 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium ChlorideNaCl
GridModel: Quantifoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 75 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 79.0 K / Max: 79.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.75 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 215000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5.3) / Number images used: 500405
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9nuc:
CryoEM analysis of Phosphoglucose isomerase from P. aeruginosa reveals potential clinically relevant features

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