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- EMDB-62682: Cryo-EM structure of bacteriophage T1 portal-adaptor -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-62682
TitleCryo-EM structure of bacteriophage T1 portal-adaptor
Map data
Sample
  • Complex: Escherichia phage T1
    • Protein or peptide: adaptor protein
    • Protein or peptide: Putative portal protein
KeywordsPortal / adaptor / phage / VIRAL PROTEIN
Function / homologyProtein of unknown function DUF4054 / Protein of unknown function (DUF4054) / Protein of unknown function DUF1073 / Phage portal protein / Uncharacterized protein / Putative portal protein
Function and homology information
Biological speciesEscherichia phage T1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: The in situ structure of T-series T1 reveals a conserved Lambda-like tail tip
Authors: Chen Y / Liu HR
History
DepositionDec 11, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62682.png

Downloads & links

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Map

FileDownload / File: emd_62682.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.16
Minimum - Maximum-9.203167000000001 - 19.290665000000001
Average (Standard dev.)0.0041531473 (±0.8677948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 489.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62682_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_62682_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 : Escherichia phage T1

EntireName: Escherichia phage T1 (virus)
Components
  • Complex: Escherichia phage T1
    • Protein or peptide: adaptor protein
    • Protein or peptide: Putative portal protein

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Supramolecule #1: Escherichia phage T1

SupramoleculeName: Escherichia phage T1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T1 (virus)

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Macromolecule #1: adaptor protein

MacromoleculeName: adaptor protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 15.455856 KDa
SequenceString:
MNQETLIAVV EQMRKLVPAL RKVPDETLYA WVEMAELFVC QKTFKDAYVK ALALYALHLA FLDGALKGED EDLESYSRRV TSFSLSGEF SQTFGEVTKN QSGDMMLSTP WGKMFEQLKA RRRGRFALMT GLRGGCH

UniProtKB: Uncharacterized protein

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Macromolecule #2: Putative portal protein

MacromoleculeName: Putative portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 48.073895 KDa
SequenceString: MKIVKHDGYN DIFNGGADGS PKPFFMSDAS YHVGSFYNDN ATAKRIVDVI PEEMVTAGFK MSGVKDEKEF KSLWDSYKLD SSLVDLLCW ARLYGGAAMV AIIKDNRMLT SQAKPGAKLE GVRVYDRFAI TVEKRVTNAR SPRYGEPEIY KVSPGDNMQP Y LIHHSRVF ...String:
MKIVKHDGYN DIFNGGADGS PKPFFMSDAS YHVGSFYNDN ATAKRIVDVI PEEMVTAGFK MSGVKDEKEF KSLWDSYKLD SSLVDLLCW ARLYGGAAMV AIIKDNRMLT SQAKPGAKLE GVRVYDRFAI TVEKRVTNAR SPRYGEPEIY KVSPGDNMQP Y LIHHSRVF IADGERVAQQ ARKQNQGWGA SVLNKSLIDA ICDYDYCESL ATQILRRKQQ AVWKVKGLAE MCDDDDAQYA AR LRLAQVD DNSGVGRAIG IDAETEEYDV LNSDISGVPE FLSSKMDRIV SLSGIHEIII KNKNVGGVSA SQNTALETFY KLV DRKREE DYRPLLEFLL PFIVDEEEWS IEFEPLSVPS KKEESEITKN NVESVTKAIT EQIIDLEEAR DTLRSIAPEF KLKD GNNIN IREPEETTEP EPGLGEKLED EN

UniProtKB: Putative portal 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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78790
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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