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- EMDB-47469: Cryo-EM map of homodecameric TraT -

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Basic information

Entry
Database: EMDB / ID: EMD-47469
TitleCryo-EM map of homodecameric TraT
Map data
Sample
  • Complex: TraT
    • Protein or peptide: TraT complement resistance protein
KeywordsMembrane protein involved in surface exclusion / MEMBRANE PROTEIN
Function / homologyEnterobacterial TraT complement resistance / Enterobacterial TraT complement resistance protein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / TraT complement resistance protein
Function and homology information
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsLundgren CAK / Lea S / Deme J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural and mutational analysis of surface exclusion protein TraT
Authors: Chen N / Lundgren CAK / Berks B / Lea S / Bykus A
History
DepositionOct 23, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47469.png

Downloads & links

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Map

FileDownload / File: emd_47469.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.28418976 - 1.0844675
Average (Standard dev.)0.0006740892 (±0.023735829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47469_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_47469_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47469_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47469_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 : TraT

EntireName: TraT
Components
  • Complex: TraT
    • Protein or peptide: TraT complement resistance protein

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Supramolecule #1: TraT

SupramoleculeName: TraT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: TraT complement resistance protein

MacromoleculeName: TraT complement resistance protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 27.668051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CGAMSTAIKK RNLEVKTQMS ETIWLEPASE RTVFLQIKNT SDKDMSGLQG KIADAVKAKG YQVVTSPDKA YYWIQANVLK ADKMDLRES QGWLNRGYEG AAVGAALGAG ITGYNSNSAG ATLGVGLAAG LVGMAADAMV EDVNYTMITD VQIAERTKAT V TTDNVAAL ...String:
CGAMSTAIKK RNLEVKTQMS ETIWLEPASE RTVFLQIKNT SDKDMSGLQG KIADAVKAKG YQVVTSPDKA YYWIQANVLK ADKMDLRES QGWLNRGYEG AAVGAALGAG ITGYNSNSAG ATLGVGLAAG LVGMAADAMV EDVNYTMITD VQIAERTKAT V TTDNVAAL RQGTSGAKIQ TSTETGNQHK YQTRVVSNAN KVNLKFEEAK PVLEDQLAKS IANILMDIGI NGTSAWSHPQ FE KGGGSGG GSGGSAWSHP QFEK

UniProtKB: TraT complement resistance protein

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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: 8
Component:
ConcentrationNameFormula
100.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
0.02 %DDM

Details: 100 mM Tris-HCl, 150 mM NaCl, 0.02% DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.015 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3979


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementOverall B value: 74.55 / Target criteria: CC
Output model

PDB-9e2v:
Cryo-EM map of homodecameric TraT

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