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- EMDB-0045: Negative stain EM map of the inner membrane protein GspF (XcpS) o... -

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Basic information

Entry
Database: EMDB / ID: EMD-0045
TitleNegative stain EM map of the inner membrane protein GspF (XcpS) of the bacterial type II secretion systemType II secretion system
Map dataFinal map after 3D refinement (Relion) low-pass filtered to 2nm.
Sample
  • Complex: fusion protein of the His-HaloTag and XcpS
    • Protein or peptide: His-HaloTag-XcpS
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsVan Putte W / Savvides S
Funding support Belgium, Germany, 3 items
OrganizationGrant numberCountry
Research Foundation - FlandersIWT-Flanders Belgium
Research Foundation - FlandersGOA Belgium
German Research FoundationSofja Kovalevskaja Award Germany
CitationJournal: To Be Published
Title: The inner membrane protein GspF of the bacterial type II secretion system adopts a dimeric structure to mediate pseudopilus biogenesis
Authors: Van Putte W / Savvides S / Kudryashev M / De Vos T
History
DepositionJun 4, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseJun 19, 2019-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0045.png

Downloads & links

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Map

FileDownload / File: emd_0045.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map after 3D refinement (Relion) low-pass filtered to 2nm.
Voxel sizeX=Y=Z: 2.29 Å
Density
Contour LevelBy EMDB: 0.0175 / Movie #1: 0.005
Minimum - Maximum-0.015363826 - 0.05337277
Average (Standard dev.)0.0005494566 (±0.005350336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 229.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.292.292.29
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z229.000229.000229.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0150.0530.001

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Supplemental data

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Sample components

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Entire : fusion protein of the His-HaloTag and XcpS

EntireName: fusion protein of the His-HaloTag and XcpS
Components
  • Complex: fusion protein of the His-HaloTag and XcpS
    • Protein or peptide: His-HaloTag-XcpS

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Supramolecule #1: fusion protein of the His-HaloTag and XcpS

SupramoleculeName: fusion protein of the His-HaloTag and XcpS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: His-HaloTag-XcpS

MacromoleculeName: His-HaloTag-XcpS / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHGS EIGTGFPFD P HYVEVLGE RM HYVDVGP RDG TPVLFL HGNP TSSYV WRNII PHVA PTHRCI APD LIGMGKS DK PDLGYFFD D HVRFMDAFI EALGLEEVVL VIHDWGSAL G FHWAKRNP ER VKGIAFM EFI RPIPTW DEWP EFARE ...String:
MAHHHHHHGS EIGTGFPFD P HYVEVLGE RM HYVDVGP RDG TPVLFL HGNP TSSYV WRNII PHVA PTHRCI APD LIGMGKS DK PDLGYFFD D HVRFMDAFI EALGLEEVVL VIHDWGSAL G FHWAKRNP ER VKGIAFM EFI RPIPTW DEWP EFARE TFQAF RTTD VGRKLI IDQ NVFIEGT LP MGVVRPLT E VEMDHYREP FLNPVDREPL WRFPNELPI A GEPANIVA LV EEYMDWL HQS PVPKLL FWGT PGVLI PPAEA ARLA KSLPNC KAV DIGPGLN LL QEDNPDLI G SEIARWLST LGSSGLEVLF QGPGLSARD L ALVTRQLA TL VQAALPI EEA LRAAAA QSTS QRIQS MLLAV RAKV LEGHSL AGS LREFPTA FP ELYRATVA A GEHAGHLGP VLEQLADYTE QRQQSRQKI Q LALLYPVI LM VASLAIV GFL LGYVVP DVVR VFIDS GQTLP LLTR VLIGVS DWV KAWGALA FV AAIGGVIG F RYALRKDAF RERWHGFLLR VPLVGRLVR S TDTARFAS TL AILTRSG VPL VEALAI AAEV IANRI IRNEV VKAA QKVREG ASL TRSLEAT GQ FPPMMLHM I ASGERSGEL DQMLARTARN QENDLAAQI G LMVGLFEP FM LIFMGAV VLV IVLAIL LPIL SLNQL VG

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 1400
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 2.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2522

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