[English] 日本語
Yorodumi
- PDB-9ld7: The capsid of mature phage N4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ld7
TitleThe capsid of mature phage N4
Components
  • 32 kDa protein
  • Major capsid protein
KeywordsVIRUS / Complex
Function / homologyPhage capsid protein / viral capsid / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 32 kDa protein / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage N4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu, H. / Chen, W.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
National Natural Science Foundation of China (NSFC)32271329 China
National Natural Science Foundation of China (NSFC)32071262 China
CitationJournal: Structure / Year: 2025
Title: Asymmetric structure of podophage N4 from the Schitoviridae family reveals a type of tube-sheath short-tail architecture.
Authors: Jing Zheng / Hao Pang / Hao Xiao / Junquan Zhou / Zhonghua Liu / Wenyuan Chen / Hongrong Liu /
Abstract: The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented ...The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented by podophage N4, exhibits a different tail architecture that remains poorly understood. In this study, we employed cryoelectron microscopy (cryo-EM) to determine the atomic structures of mature and empty podophage N4 particles. The N4 tail, which is connected to the head by a portal and flanked by 12 fibers, comprises an adaptor, a 12-fold extended tail tube encircled by a 6-fold tail sheath, and a plug. The extended tail sheath is composed of two proteins, gp65 and gp64. Furthermore, we identified two distinct tail conformations in the mature podophage N4. Our structures provide insights into the mechanisms of ejection and early transcription of podophage N4, as well as for N4-like phages and CrAssphages.
History
DepositionJan 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein


Theoretical massNumber of molelcules
Total (without water)484,29112
Polymers484,29112
Non-polymers00
Water00
1
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein
x 60


Theoretical massNumber of molelcules
Total (without water)29,057,463720
Polymers29,057,463720
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
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein
x 5


  • icosahedral pentamer
  • 2.42 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,421,45560
Polymers2,421,45560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
E: 32 kDa protein
G: 32 kDa protein
H: Major capsid protein
B: Major capsid protein
J: Major capsid protein
C: Major capsid protein
D: Major capsid protein
I: Major capsid protein
F: Major capsid protein
K: Major capsid protein
L: 32 kDa protein
x 6


  • icosahedral 23 hexamer
  • 2.91 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,905,74672
Polymers2,905,74672
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
Major capsid protein / Gene product 56 / gp56 / Major head protein


Mass: 44074.816 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: Q859Q5
#2: Protein 32 kDa protein / gp17


Mass: 29205.900 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage N4 (virus) / References: UniProt: A0MZA7
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Escherichia phage N4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage N4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 4000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18940 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334611
ELECTRON MICROSCOPYf_angle_d0.53946926
ELECTRON MICROSCOPYf_dihedral_angle_d4.4254761
ELECTRON MICROSCOPYf_chiral_restr0.0445391
ELECTRON MICROSCOPYf_plane_restr0.0066042

+
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