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- EMDB-30138: Packing Bacteriophage T7 portal protein GP8 -

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Basic information

Entry
Database: EMDB / ID: EMD-30138
TitlePacking Bacteriophage T7 portal protein GP8
Map dataPacking Phage GP8
Sample
  • Complex: Packing Bacteriophage T7 portal protein GP8
    • Protein or peptide: Portal protein
Keywordspacking / phage / portal / protein / STRUCTURAL PROTEIN
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bp0
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bp0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30138.png

Downloads & links

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Map

FileDownload / File: emd_30138.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPacking Phage GP8
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 320 pix.
= 406.4 Å		1.27 Å/pix.
x 320 pix.
= 406.4 Å		1.27 Å/pix.
x 320 pix.
= 406.4 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: 10
Minimum - Maximum-25.084161999999999 - 34.25121
Average (Standard dev.)0.03809688 (±1.8523066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 406.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-25.08434.2510.038

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Supplemental data

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Sample components

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Entire : Packing Bacteriophage T7 portal protein GP8

EntireName: Packing Bacteriophage T7 portal protein GP8
Components
  • Complex: Packing Bacteriophage T7 portal protein GP8
    • Protein or peptide: Portal protein

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Supramolecule #1: Packing Bacteriophage T7 portal protein GP8

SupramoleculeName: Packing Bacteriophage T7 portal protein GP8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T7 (virus)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 59.173984 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV ...String:
MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV QRDAFGNVLQ MVTRDQIAFG ALPEDIRKAV EGQGGEKKAD ETIDVYTHIY LDEDSGEYLR YEEVEGMEVQ GS DGTYPKE ACPYIPIRMV RLDGESYGRS YIEEYLGDLR SLENLQEAIV KMSMISSKVI GLVNPAGITQ PRRLTKAQTG DFV TGRPED ISFLQLEKQA DFTVAKAVSD AIEARLSFAF MLNSAVQRTG ERVTAEEIRY VASELEDTLG GVYSILSQEL QLPL VRVLL KQLQATQQIP ELPKEAVEPT ISTGLEAIGR GQDLDKLERC VTAWAALAPM RDDPDINLAM IKLRIANAIG IDTSG ILLT EEQKQQKMAQ QSMQMGMDNG AAALAQGMAA QATASPEAMA AAADSVGLQP GI

UniProtKB: 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
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 27.0 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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84318
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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