[English] 日本語
Yorodumi
- PDB-5wk1: Structure of the major capsid protein and the capsid stabilizing ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wk1
TitleStructure of the major capsid protein and the capsid stabilizing protein of the marine siphovirus TW1
Components
  • Capsid Stabilizing Protein
  • Major Capsid Protein
KeywordsVIRUS / Major Capsid Protein / Capsid Stabilizing Protein / HK 97 fold / Decoration Protein
Function / homologyviral capsid / Putative coat protein / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas phage TW1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, Z. / Rossmann, M.G.
Funding support United States, 1items
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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8854
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8854
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Capsid Stabilizing Protein
L: Capsid Stabilizing Protein
Y: Capsid Stabilizing Protein
M: Capsid Stabilizing Protein
S: Capsid Stabilizing Protein
Z: Capsid Stabilizing Protein
K: Capsid Stabilizing Protein
A: Major Capsid Protein
B: Major Capsid Protein
C: Major Capsid Protein
D: Major Capsid Protein
E: Major Capsid Protein
F: Major Capsid Protein
G: Major Capsid Protein


Theoretical massNumber of molelcules
Total (without water)378,46014
Polymers378,46014
Non-polymers00
Water0
1
X: Capsid Stabilizing Protein
L: Capsid Stabilizing Protein
Y: Capsid Stabilizing Protein
M: Capsid Stabilizing Protein
S: Capsid Stabilizing Protein
Z: Capsid Stabilizing Protein
K: Capsid Stabilizing Protein
A: Major Capsid Protein
B: Major Capsid Protein
C: Major Capsid Protein
D: Major Capsid Protein
E: Major Capsid Protein
F: Major Capsid Protein
G: Major Capsid Protein
x 60


Theoretical massNumber of molelcules
Total (without water)22,707,612840
Polymers22,707,612840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
X: Capsid Stabilizing Protein
L: Capsid Stabilizing Protein
Y: Capsid Stabilizing Protein
M: Capsid Stabilizing Protein
S: Capsid Stabilizing Protein
Z: Capsid Stabilizing Protein
K: Capsid Stabilizing Protein
A: Major Capsid Protein
B: Major Capsid Protein
C: Major Capsid Protein
D: Major Capsid Protein
E: Major Capsid Protein
F: Major Capsid Protein
G: Major Capsid Protein
x 5


  • icosahedral pentamer
  • 1.89 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,892,30170
Polymers1,892,30170
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
X: Capsid Stabilizing Protein
L: Capsid Stabilizing Protein
Y: Capsid Stabilizing Protein
M: Capsid Stabilizing Protein
S: Capsid Stabilizing Protein
Z: Capsid Stabilizing Protein
K: Capsid Stabilizing Protein
A: Major Capsid Protein
B: Major Capsid Protein
C: Major Capsid Protein
D: Major Capsid Protein
E: Major Capsid Protein
F: Major Capsid Protein
G: Major Capsid Protein
x 6


  • icosahedral 23 hexamer
  • 2.27 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,270,76184
Polymers2,270,76184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
Capsid Stabilizing Protein


Mass: 15017.777 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas phage TW1 (virus) / References: UniProt: S5MS27
#2: Protein
Major Capsid Protein


Mass: 39047.965 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas phage TW1 (virus) / References: UniProt: S5M825

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Pseudoalteromonas phage TW1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudoalteromonas phage TW1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2100 mMsodium chlorideNaClSodium chloride1
38 mMmagnesium sulfateMgSO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 400 divisions/in. / Grid type: Ted Pella Inc, Lacey Carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K
Image recordingElectron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
4jsprctfit2CTF correction
10jsprinitial Euler assignment
11jsprfinal Euler assignment
13jspr3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 16216
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8663 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more