[English] 日本語
- PDB-6i9e: Thermophage P23-45 empty expanded capsid -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6i9e
TitleThermophage P23-45 empty expanded capsid
  • Auxiliary protein
  • Major head protein
KeywordsVIRUS / bacteriophage / thermophage / caudovirales / siphoviridae / capsid / auxiliary / HK97 / virus
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / Uncharacterized protein / Major head protein
Function and homology information
Specimen sourceThermus virus P23-45 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.74 Å resolution
AuthorsBayfield, O.W. / Klimuk, E. / Winkler, D.C. / Hesketh, E.L. / Chechik, M. / Cheng, N. / Dykeman, E.C. / Minakhin, L. / Ranson, N.A. / Severinov, K. / Steven, A.C. / Antson, A.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.
Authors: Oliver W Bayfield / Evgeny Klimuk / Dennis C Winkler / Emma L Hesketh / Maria Chechik / Naiqian Cheng / Eric C Dykeman / Leonid Minakhin / Neil A Ranson / Konstantin Severinov / Alasdair C Steven / Alfred A Antson
Abstract: Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic ...Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 23, 2018 / Release: Feb 6, 2019

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4433
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: Auxiliary protein
I: Auxiliary protein
J: Auxiliary protein
K: Auxiliary protein
L: Auxiliary protein
M: Auxiliary protein
N: Auxiliary protein

Theoretical massNumber of molelcules
Total (without water)443,39214

  • idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, LC-MS/MS of purified capsids
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)65050
ΔGint (kcal/M)-359
Surface area (Å2)193160


#1: Protein/peptide
Major head protein

Mass: 46680.754 Da / Num. of mol.: 7 / Source: (natural) Thermus virus P23-45 (bacteriophage) / Cell line: Thermus thermophilus HB8 / References: UniProt: A7XXC2
#2: Protein/peptide
Auxiliary protein

Mass: 16661.002 Da / Num. of mol.: 7 / Source: (natural) Thermus virus P23-45 (bacteriophage) / Cell line: Thermus thermophilus HB8 / References: UniProt: A7XXC1

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Thermus phage P2345 / Type: VIRUS / Entity ID: 1, 2 / Source: NATURAL
Molecular weightValue: 26.57 MDa / Experimental value: NO
Source (natural)Organism: Thermus phage P2345 (bacteriophage)
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Thermus thermophilus HB8
Virus shellTriangulation number (T number): 7
Buffer solutionpH: 8
Buffer component
IDConc.FormulaBuffer ID
1100 mMNaCl1
220 mMTris-HCl1
310 mMMgCL21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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: 75000 / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 99 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)


SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
2EPUimage acquisition
4CTFFINDCTF correction
9PHENIXmodel refinement
10Cootmodel refinement
11RELIONinitial Euler assignment
12RELIONfinal Euler assignment
14RELION3D reconstruction
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 2372 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Least-squares processHighest resolution: 3.74 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00732284
ELECTRON MICROSCOPYf_angle_d0.90444044
ELECTRON MICROSCOPYf_dihedral_angle_d10.44019152
ELECTRON MICROSCOPYf_chiral_restr0.0604739
ELECTRON MICROSCOPYf_plane_restr0.0085761

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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