[English] 日本語
Yorodumi
- PDB-9yf4: N4 Full Virion C6 Tail -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yf4
TitleN4 Full Virion C6 Tail
Components
  • 16.5 kDa protein
  • 30 kDa protein
  • 60 kDa protein
  • Gp54
  • Gp64
  • Non-contractile tail sheath
  • Probable portal protein
KeywordsVIRAL PROTEIN / dodecamer / bacteriophage portal
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell
Similarity search - Function
: / : / Non-contractile tail sheath N-terminal domain / Non-contractile tail sheath protein TIM barrel / : / SU10 adaptor protein / : / Phage SU10 portal protein / Leucine-rich repeat profile. / Leucine-rich repeat
Similarity search - Domain/homology
Probable portal protein / Gp64 / Non-contractile tail sheath / 60 kDa protein / 30 kDa protein / 16.5 kDa protein / Gp54
Similarity search - Component
Biological speciesEscherichia phage N4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBellis, N.F. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Architecture of the giant RNA polymerase ejected from the coliphage N4 Capsid
Authors: Bellis, N.F. / Lokareddy, R.K. / Kizziah, J.L. / Cooper, S.L. / Schneider, D.A. / Forti, F. / Briani, F. / Cingolani, G.
History
DepositionSep 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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
AA: 30 kDa protein
AB: 30 kDa protein
LA: Non-contractile tail sheath
PA: Probable portal protein
SA: Gp64
TA: Gp54
XA: 60 kDa protein
XB: 60 kDa protein
YA: 60 kDa protein
YB: 60 kDa protein
ZA: 60 kDa protein
ZB: 60 kDa protein
PB: Probable portal protein
TB: Gp54
AC: 30 kDa protein
AD: 30 kDa protein
LB: Non-contractile tail sheath
PC: Probable portal protein
SB: Gp64
TC: Gp54
XC: 60 kDa protein
XD: 60 kDa protein
YC: 60 kDa protein
YD: 60 kDa protein
ZC: 60 kDa protein
ZD: 60 kDa protein
PD: Probable portal protein
TD: Gp54
AE: 30 kDa protein
AF: 30 kDa protein
LC: Non-contractile tail sheath
PE: Probable portal protein
SC: Gp64
TE: Gp54
XE: 60 kDa protein
XF: 60 kDa protein
YE: 60 kDa protein
YF: 60 kDa protein
ZE: 60 kDa protein
ZF: 60 kDa protein
PF: Probable portal protein
TF: Gp54
AG: 30 kDa protein
AH: 30 kDa protein
LD: Non-contractile tail sheath
PG: Probable portal protein
SD: Gp64
TG: Gp54
XG: 60 kDa protein
XH: 60 kDa protein
YG: 60 kDa protein
YH: 60 kDa protein
ZG: 60 kDa protein
ZH: 60 kDa protein
PH: Probable portal protein
TH: Gp54
AI: 30 kDa protein
AJ: 30 kDa protein
LE: Non-contractile tail sheath
PI: Probable portal protein
SE: Gp64
TI: Gp54
XI: 60 kDa protein
XJ: 60 kDa protein
YI: 60 kDa protein
YJ: 60 kDa protein
ZI: 60 kDa protein
ZJ: 60 kDa protein
PJ: Probable portal protein
TJ: Gp54
AK: 30 kDa protein
AL: 30 kDa protein
LF: Non-contractile tail sheath
PK: Probable portal protein
SF: Gp64
TK: Gp54
XK: 60 kDa protein
XL: 60 kDa protein
YK: 60 kDa protein
YL: 60 kDa protein
ZK: 60 kDa protein
ZL: 60 kDa protein
PL: Probable portal protein
TL: Gp54
OA: 16.5 kDa protein
OB: 16.5 kDa protein
OC: 16.5 kDa protein
OD: 16.5 kDa protein
OE: 16.5 kDa protein
OF: 16.5 kDa protein
OG: 16.5 kDa protein
OH: 16.5 kDa protein
OI: 16.5 kDa protein
OJ: 16.5 kDa protein
OK: 16.5 kDa protein
OL: 16.5 kDa protein


Theoretical massNumber of molelcules
Total (without water)5,272,63996
Polymers5,272,63996
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 7 types, 96 molecules AAABACADAEAFAGAHAIAJAKALLALBLCLDLELFPAPBPCPDPEPFPGPHPIPJPKPL...

#1: Protein
30 kDa protein


Mass: 27192.412 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE9
#2: Protein
Non-contractile tail sheath / Gene product 65 / Gp65


Mass: 154255.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE7
#3: Protein
Probable portal protein / 94 kDa protein / Gene product 59 / gp59 / Head-to-tail connector


Mass: 85642.523 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE1
#4: Protein
Gp64


Mass: 48100.742 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE6
#5: Protein
Gp54


Mass: 32438.443 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: Q859Q3
#6: Protein ...
60 kDa protein


Mass: 58943.914 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE8
#7: Protein
16.5 kDa protein


Mass: 16103.577 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: Q859Q1

-
Details

Has protein modificationY

-
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: #1 / Source: NATURAL
Source (natural)Organism: Escherichia phage N4 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Escherichia coli str. K-12 substr. MG1655
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16320 / 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