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- EMDB-36746: CryoEM structure of the Salmonella effector inositol phosphate ph... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36746
TitleCryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB
Map data
Sample
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: Inositol phosphate phosphatase SopB
KeywordsType III secretion system / inositol phosphate phosphatase / bacteria effector / LIPID BINDING PROTEIN
Function / homology
Function and homology information


symbiont-containing vacuole / negative regulation of signaling / regulation of protein kinase activity / lipid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / molecular function activator activity / positive regulation of DNA replication / cell periphery / negative regulation of cell growth
Similarity search - Function
Phosphatase IpgD/SopB / Enterobacterial virulence protein IpgD
Similarity search - Domain/homology
Inositol phosphate phosphatase SopB
Similarity search - Component
Biological speciesSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsJiang WX / Cheng XQ / Wu M / Ma LX
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB
Authors: Jiang WX / Cheng XQ / Wu M / Ma LX / Xing Q
History
DepositionJul 5, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36746.png

Downloads & links

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Map

FileDownload / File: emd_36746.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 480 pix.
= 271.68 Å		0.57 Å/pix.
x 480 pix.
= 271.68 Å		0.57 Å/pix.
x 480 pix.
= 271.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.566 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0176
Minimum - Maximum-0.080559246 - 0.22355361
Average (Standard dev.)-0.00030728712 (±0.007457731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 271.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36746_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36746_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homohexamer of inositol phosphate phosphatase SopB

EntireName: Homohexamer of inositol phosphate phosphatase SopB
Components
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: Inositol phosphate phosphatase SopB

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Supramolecule #1: Homohexamer of inositol phosphate phosphatase SopB

SupramoleculeName: Homohexamer of inositol phosphate phosphatase SopB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Macromolecule #1: Inositol phosphate phosphatase SopB

MacromoleculeName: Inositol phosphate phosphatase SopB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 55.05268 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: QHQKASNHSL HNLYNLQRDL LTVAATVLGK QDPVLTSMAN QMELAKVKAD RPATKQEEAA AKALKKNLIE LIAARTQQQD GLPAKEAHR FAAVAFRDAQ VKQLNNQPWQ TIKNTLTHNG HHYTNTQLPA AEMKIGAKDI FPSAYEGKGV CSWDTKNIHH A NNLWMSTV ...String:
QHQKASNHSL HNLYNLQRDL LTVAATVLGK QDPVLTSMAN QMELAKVKAD RPATKQEEAA AKALKKNLIE LIAARTQQQD GLPAKEAHR FAAVAFRDAQ VKQLNNQPWQ TIKNTLTHNG HHYTNTQLPA AEMKIGAKDI FPSAYEGKGV CSWDTKNIHH A NNLWMSTV SVHEDGKDKT LFCGIRHGVL SPYHEKDPLL RHVGAENKAK EVLTAALFSK PELLNKALAG EAVSLKLVSV GL LTASNIF GKEGTMVEDQ MRAWQSLTQP GKMIHLKIRN KDGDLQTVKI KPDVAAFNVG VNELALKLGF GLKASDSYNA EAL HQLLGN DLRPEARPGG WVGEWLAQYP DNYEVVNTLA RQIKDIWKNN QHHKDGGEPY KLAQRLAMLA HEIDAVPAWN CKSG KDRTG MMDSEIKREI ISLHQTHMLS APGSLPDSGG QKIFQKVLLN SGNLEIQKQN TGGAGNKVMK NLSPEVLNLS YQKRV GDEN IWQSVKGISS LITS

UniProtKB: Inositol phosphate phosphatase SopB

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241912
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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