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- EMDB-8854: Structure of the major capsid protein and the capsid stabilizing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8854
TitleStructure of the major capsid protein and the capsid stabilizing protein of the marine siphovirus TW1
Map dataicosahedral reconstruction of marine Siphophage TW1 head
Sample
  • Virus: Pseudoalteromonas phage TW1 (virus)
    • Protein or peptide: Capsid Stabilizing Protein
    • Protein or peptide: Major Capsid Protein
KeywordsMajor Capsid Protein / Capsid Stabilizing Protein / HK 97 fold / Decoration Protein / VIRUS
Function / homologyviral capsid / Putative coat protein / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas phage TW1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang Z / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1515260 United States
CitationJournal: Structure / Year: 2018
Title: Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes.
Authors: Zhiqing Wang / Stephen C Hardies / Andrei Fokine / Thomas Klose / Wen Jiang / Byung Cheol Cho / Michael G Rossmann /
Abstract: Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of ...Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of most of these proteins have been predicted by bioinformatic methods. A 3.6 Å resolution cryoelectron microscopy map of the icosahedrally averaged TW1 head showed the atomic structures of the major capsid protein, gp57, and the capsid-stabilizing protein, gp56. The gp57 structure is similar to that of the phage HK97 capsid protein. The gp56 protein has two domains, each having folds similar to that of the N-terminal part of phage λ gpD, indicating a common ancestry. The first gp56 domain clamps adjacent capsomers together, whereas the second domain is required for trimerization. A 6-fold-averaged reconstruction of the distal part of the tail showed that TW1 has six tail spikes, which are unusual for siphophages but are similar to the podophages P22 and Sf6, suggesting a common evolutionary origin of these spikes.
History
DepositionJul 24, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseJan 17, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 4.79
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.79
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wk1
  • Surface level: 4.79
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5wk1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8854.png

Downloads & links

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Map

FileDownload / File: emd_8854.map.gz / Format: CCP4 / Size: 11.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedral reconstruction of marine Siphophage TW1 head
Voxel sizeX=Y=Z: 0.667 Å
Density
Contour LevelBy AUTHOR: 4.79 / Movie #1: 4.79
Minimum - Maximum-16.355609999999999 - 21.784884999999999
Average (Standard dev.)0.014140712 (±1.0399446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-720-720-720
Dimensions144014401440
Spacing144014401440
CellA=B=C: 960.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6670.6670.667
M x/y/z144014401440
origin x/y/z0.0000.0000.000
length x/y/z960.480960.480960.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-59-19-84
NX/NY/NZ8052101
MAP C/R/S123
start NC/NR/NS-720-720-720
NC/NR/NS144014401440
D min/max/mean-16.35621.7850.014

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Supplemental data

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Sample components

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Entire : Pseudoalteromonas phage TW1

EntireName: Pseudoalteromonas phage TW1 (virus)
Components
  • Virus: Pseudoalteromonas phage TW1 (virus)
    • Protein or peptide: Capsid Stabilizing Protein
    • Protein or peptide: Major Capsid Protein

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Supramolecule #1: Pseudoalteromonas phage TW1

SupramoleculeName: Pseudoalteromonas phage TW1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1366055 / Sci species name: Pseudoalteromonas phage TW1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid Stabilizing Protein

MacromoleculeName: Capsid Stabilizing Protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudoalteromonas phage TW1 (virus)
Molecular weightTheoretical: 15.017777 KDa
SequenceString:
MANSKNSIFV GGAGRVKQTI EGLAQSAFKP GQLLARAAGD AIDVTAKAST TYGNEFLICD DQPQTLGGGT DVAVTAGDTV QAISVLPGQ YVLLSFAATQ NVTTKGAAVA SNGDGNFKLG NPATEQTFAV TEEIINVTTA GTLVLCRAI

UniProtKB: Uncharacterized protein

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Macromolecule #2: Major Capsid Protein

MacromoleculeName: Major Capsid Protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudoalteromonas phage TW1 (virus)
Molecular weightTheoretical: 39.047965 KDa
SequenceString: MSIHFDFKNK QGKELLALNR QWNELSGYRA HAFNESVNML NNVGETFGVN GANAMQTNMQ RVDEMYRLVD STGTGEDRDW GNQTLLGRL LSQAQTVSIG KKVIESRRYS EAGRINRSMS GQTDIDMDKT KSSYQKMVIP VFDGAYGRDF RDYEAMRSEM L PALAEDSE ...String:
MSIHFDFKNK QGKELLALNR QWNELSGYRA HAFNESVNML NNVGETFGVN GANAMQTNMQ RVDEMYRLVD STGTGEDRDW GNQTLLGRL LSQAQTVSIG KKVIESRRYS EAGRINRSMS GQTDIDMDKT KSSYQKMVIP VFDGAYGRDF RDYEAMRSEM L PALAEDSE EIEFTLLDDV NDYLWNGDAK LKVDTAVWGG LKADASVAAY SLGADLTTAT EAQVVAELLA LLDVLRITNK KS GPFELYI SPQIMSNWQK LAGANTNGFM NIMAAVRALI PEFSVVEADS ALQGNQVLCS VVGTRGLHAK IGMMMSSYQV PRV MHNDPY QFVKWFAAGF QSNNSFSGLK STVYGS

UniProtKB: Putative coat 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: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
100.0 mMNaClSodium chloridesodium chloride
8.0 mMMgSO4magnesium sulfate

Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4
GridModel: Ted Pella Inc, Lacey Carbon / Mesh: 400 / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 16216
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 8663

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