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- EMDB-30137: N-teminal of mature bacteriophage T7 tail fiber protein gp17 -

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Basic information

Entry
Database: EMDB / ID: EMD-30137
TitleN-teminal of mature bacteriophage T7 tail fiber protein gp17
Map dataMature Phage GP17
Sample
  • Complex: N-teminal of mature bacteriophage T7 tail fiber protein gp17
    • Protein or peptide: N-teminal of mature bacteriophage T7 tail fiber protein gp17
Keywordsphage / portal / protein / mature / STRUCTURAL PROTEIN
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
: / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain
Similarity search - Domain/homology
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen WY / Xiao H
Funding support1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Protein Cell / Year: 2020
Title: Structural changes of a bacteriophage upon DNA packaging and maturation.
Authors: Wenyuan Chen / Hao Xiao / Xurong Wang / Shuanglin Song / Zhen Han / Xiaowu Li / Fan Yang / Li Wang / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
History
DepositionMar 20, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7boz
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7boz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30137.png

Downloads & links

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Map

FileDownload / File: emd_30137.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMature Phage GP17
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 352 pix.
= 447.04 Å		1.27 Å/pix.
x 352 pix.
= 447.04 Å		1.27 Å/pix.
x 352 pix.
= 447.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-14.838167 - 27.532070000000001
Average (Standard dev.)-0.31891695 (±0.9940423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 447.03998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z447.040447.040447.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-14.83827.532-0.319

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Supplemental data

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Sample components

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Entire : N-teminal of mature bacteriophage T7 tail fiber protein gp17

EntireName: N-teminal of mature bacteriophage T7 tail fiber protein gp17
Components
  • Complex: N-teminal of mature bacteriophage T7 tail fiber protein gp17
    • Protein or peptide: N-teminal of mature bacteriophage T7 tail fiber protein gp17

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Supramolecule #1: N-teminal of mature bacteriophage T7 tail fiber protein gp17

SupramoleculeName: N-teminal of mature bacteriophage T7 tail fiber protein gp17
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T7 (virus)

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Macromolecule #1: N-teminal of mature bacteriophage T7 tail fiber protein gp17

MacromoleculeName: N-teminal of mature bacteriophage T7 tail fiber protein gp17
type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 61.641875 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MANVIKTVLT YQLDGSNRDF NIPFEYLARK FVVVTLIGVD RKVLTINTDY RFATRTTISL TKAWGPADGY TTIELRRVTS TTDRLVDFT DGSILRAYDL NVAQIQTMHV AEEARDLTTD TIGVNNDGHL DARGRRIVNL ANAVDDRDAV PFGQLKTMNQ N SWQARNEA ...String:
MANVIKTVLT YQLDGSNRDF NIPFEYLARK FVVVTLIGVD RKVLTINTDY RFATRTTISL TKAWGPADGY TTIELRRVTS TTDRLVDFT DGSILRAYDL NVAQIQTMHV AEEARDLTTD TIGVNNDGHL DARGRRIVNL ANAVDDRDAV PFGQLKTMNQ N SWQARNEA LQFRNEAETF RNQAEGFKNE SSTNATNTKQ WRDETKGFRD EAKRFKNTAG QYATSAGNSA SAAHQSEVNA EN SATASAN SAHLAEQQAD RAEREADKLE NYNGLAGAID KVDGTNVYWK GNIHANGRLY MTTNGFDCGQ YQQFFGGVTN RYS VMEWGD ENGWLMYVQR REWTTAIGGN IQLVVNGQII TQGGAMTGQL KLQNGHVLQL ESASDKAHYI LSKDGNRNNW YIGR GSDNN NDCTFHSYVH GTTLTLKQDY AVVNKHFHVG QAVVATDGNI QGTKWGGKWL DAYLRDSFVA KSKAWTQVWS GSAGG GVSV TVSQDLRFRN IWIKCANNSW NFFRTGPDGI YFIASDGGWL RFQIHSNGLG FKNIADSRSV PNAIMVENE

UniProtKB: Tail fiber 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
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 24.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55212
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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