[English] 日本語
Yorodumi
- PDB-9swa: Adenovirus dodecahedron -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9swa
TitleAdenovirus dodecahedron
ComponentsPenton protein
KeywordsVIRUS LIKE PARTICLE / adenovirus / vaccine / dodecahedron
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / : / Penton protein
Function and homology information
Biological speciesChimpanzee adenovirus Y25
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKabasakal, B.V. / Buzas, D. / Bufton, J. / Berger-Schaffitzel, C. / Berger, I.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust210701/Z/18/Z; 106115/Z/14/Z; 202904/Z/16/Z; 206181/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R000484/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/R013764/1 United Kingdom
CitationJournal: Acs Synth Biol / Year: 2026
Title: Engineering the ADDomer Nanoparticle Vaccine Scaffold for Improved Assembly and Enhanced Stability.
Authors: Balchin, G. / Kabasakal, B.V. / Strofaldi, A. / Hall, S. / Fletcher, C. / Buzas, D. / Bufton, J.C. / Yadav, S.K.N. / Shen, D. / Garzoni, F. / Bunzel, H.A. / McManus, J.J. / Schaffitzel, C. / Berger, I.
History
DepositionOct 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 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
1: Penton protein
2: Penton protein
3: Penton protein
4: Penton protein
5: Penton protein
6: Penton protein
7: Penton protein
8: Penton protein
9: Penton protein
A: Penton protein
B: Penton protein
C: Penton protein
D: Penton protein
E: Penton protein
F: Penton protein
G: Penton protein
H: Penton protein
I: Penton protein
J: Penton protein
K: Penton protein
L: Penton protein
M: Penton protein
N: Penton protein
O: Penton protein
P: Penton protein
Q: Penton protein
R: Penton protein
S: Penton protein
T: Penton protein
V: Penton protein
W: Penton protein
X: Penton protein
Y: Penton protein
Z: Penton protein
a: Penton protein
b: Penton protein
c: Penton protein
d: Penton protein
e: Penton protein
f: Penton protein
g: Penton protein
h: Penton protein
i: Penton protein
j: Penton protein
k: Penton protein
l: Penton protein
m: Penton protein
n: Penton protein
o: Penton protein
p: Penton protein
q: Penton protein
r: Penton protein
s: Penton protein
t: Penton protein
u: Penton protein
v: Penton protein
w: Penton protein
x: Penton protein
y: Penton protein
z: Penton protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,650,75372
Polymers3,650,28460
Non-polymers46912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
Penton protein / CP-P / Penton base protein / Protein III


Mass: 60838.066 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: L2 / Production host: unidentified baculovirus / References: UniProt: G9G849
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Adenovirus dodecahedron / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 3.65 MDa / Experimental value: NO
Source (natural)Organism: Chimpanzee adenovirus Y25
Source (recombinant)Organism: unidentified baculovirus
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 44.01 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFINDCTF correction
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147098 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

+
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