[English] 日本語
Yorodumi
- PDB-9vel: The composite cryo-EM structure of bacteriophage SPO1 capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vel
TitleThe composite cryo-EM structure of bacteriophage SPO1 capsid
Components
  • Gp2.7
  • Gp29.2
  • Gp36.3
  • Gp6.1
KeywordsVIRUS / SPO1 / Phage / Capsid
Function / homologyProtein of unknown function DUF5309 / SU10 major capsid protein / membrane / Gp36.3 / Gp29.2 / Gp2.7 / Gp6.1
Function and homology information
Biological speciesBacillus phage SPO1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhao, X. / Wang, A. / Wang, Y. / Kang, Y. / Shao, Q. / Li, L. / Zheng, Y. / Hu, H. / Li, X. / Fan, H. ...Zhao, X. / Wang, A. / Wang, Y. / Kang, Y. / Shao, Q. / Li, L. / Zheng, Y. / Hu, H. / Li, X. / Fan, H. / Cai, C. / Liu, B. / Fang, Q.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Capsid structure of phage SPO1 reveals novel minor capsid proteins and insights into capsid stabilization
Authors: Zhao, X. / Wang, A. / Wang, Y. / Kang, Y. / Shao, Q. / Li, L. / Zheng, Y. / Hu, H. / Li, X. / Fan, H. / Cai, C. / Liu, B. / Fang, Q.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3


Theoretical massNumber of molelcules
Total (without water)919,66622
Polymers919,66622
Non-polymers00
Water00
1
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3
x 60


Theoretical massNumber of molelcules
Total (without water)55,179,9371320
Polymers55,179,9371320
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
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3
x 5


  • icosahedral pentamer
  • 4.6 MDa, 110 polymers
Theoretical massNumber of molelcules
Total (without water)4,598,328110
Polymers4,598,328110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3
x 6


  • icosahedral 23 hexamer
  • 5.52 MDa, 132 polymers
Theoretical massNumber of molelcules
Total (without water)5,517,994132
Polymers5,517,994132
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
Gp6.1


Mass: 51445.043 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2N7
#2: Protein
Gp29.2


Mass: 19837.922 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2J1
#3: Protein Gp2.7


Mass: 6380.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2M7
#4: Protein Gp36.3


Mass: 10812.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2H5
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bacillus phage SPO1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus phage SPO1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 1050 nm
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 26.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFIND4CTF correction
10RELION4initial Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626340 / 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