[English] 日本語
Yorodumi
- PDB-9yd0: Structure of the Adenovirus-7 VLP, Class 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yd0
TitleStructure of the Adenovirus-7 VLP, Class 1
Components
  • Hexon protein
  • Hexon-interlacing protein IX
  • Pre-hexon-linking protein IIIa
  • Pre-hexon-linking protein VIII
  • Pre-protein VI
KeywordsVIRUS LIKE PARTICLE / Adenovirus / vaccine / VLP
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / viral procapsid / lysis of host organelle involved in viral entry into host cell / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / viral procapsid / lysis of host organelle involved in viral entry into host cell / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon protein / Hexon-interlacing protein IX / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-hexon-linking protein IIIa
Similarity search - Component
Biological speciesHuman adenovirus 7
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKhayat, R. / Madoo, K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5SC1GM139701 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5G12MD007603-30 United States
Simons Foundation349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Department of Defense (DOD, United States)W81XH19C0169 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Structure of Human adenovirus 7 virus-like particles, a platform for developing nanotherapeutics and studying capsid assembly.
Authors: Madoo, K. / Mazboudi, R. / Islam, Z.M. / Luo, J. / Kuschner, R.A. / Gottlieb, P. / Dennehy, J.J. / Abzalimov, R.R. / Galarza, J.M. / Khayat, R.
History
DepositionSep 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein IX
Q: Hexon-interlacing protein IX
R: Hexon-interlacing protein IX
S: Hexon-interlacing protein IX
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
Y: Pre-protein VI
Z: Pre-protein VI


Theoretical massNumber of molelcules
Total (without water)1,655,22427
Polymers1,655,22427
Non-polymers00
Water00
1


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

-
Components

#1: Protein
Pre-protein VI / pVI


Mass: 27178.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L3 / Cell (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q5EY64
#2: Protein
Hexon protein / CP-H / Protein II


Mass: 105807.125 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: P36851
#3: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 65798.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L1 / Production host: Homo sapiens (human) / References: UniProt: Q5EY68
#4: Protein
Hexon-interlacing protein IX / Protein IX


Mass: 13125.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Due to the low quality of map in certain regions, the identites of some of the amino acids in the model were left as unknown (UNK).
Source: (gene. exp.) Human adenovirus 7 / Gene: IX / Production host: Homo sapiens (human) / References: UniProt: P68971
#5: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24902.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L4 / Production host: Homo sapiens (human) / References: UniProt: Q5EY56
Has protein modificationN
Sequence detailsMany residues of chains P, Q, R, and S, comprised of entity 4 (Protein IX) were not identified, and ...Many residues of chains P, Q, R, and S, comprised of entity 4 (Protein IX) were not identified, and modeled as UNK. The actual sequence is: MSGSASFEGGVFSPYLTGRLPPWAGVRQNVMGSTVDGRPVQPANSSTLTYATLSSSPLDAAAAAAATAAANTILGMGYYG SIVANSSSSNNPSTLAEDKLLVLLAQLEALTQRLGELSKQVAQLREQTESAVATAKSK

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Adenovirus 7 Virus-like particles / Type: COMPLEX / Details: Adenovirus 7 Virus-like particles / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 18.2 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 7
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-293
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 50 sec. / Electron dose: 53.35 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13608 / Details: Not all images had particles.
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.13particle selectionManual picking
2Leginonimage acquisition
4cryoSPARC4.13CTF correction
7UCSF Chimera1.19model fittingManually fitted as rigid body
9cryoSPARC4.13initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIX1.19model refinementWeight was placed on geometry
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 360841 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: phenix.real_space_refine 1.19.2_4158
Atomic model buildingSource name: AlphaFold / Type: in silico 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