[English] 日本語
Yorodumi
- PDB-6qi5: Near Atomic Structure of an Atadenovirus Shows a possible gene du... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qi5
TitleNear Atomic Structure of an Atadenovirus Shows a possible gene duplication event and Intergenera Variations in Cementing Proteins
Components
  • Hexon protein
  • PIIIa
  • Penton protein
  • Pre-hexon-linking protein VIII
  • Protein LH3
KeywordsVIRUS / adenovirus atadenovirus virus evolution
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / endocytosis involved in viral entry into host cell / viral capsid / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell / nucleus
Similarity search - Function
Adenovirus large t-antigen, E1B 55kDa protein / Adenovirus EB1 55K protein / large t-antigen / : / 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 / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal ...Adenovirus large t-antigen, E1B 55kDa protein / Adenovirus EB1 55K protein / large t-antigen / : / 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 / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Penton protein / Pre-hexon-linking protein VIII / Protein LH3 / PIIIa / Hexon protein
Similarity search - Component
Biological speciesLizard adenovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCondezo, G.N. / Marabini, R. / Gomez-Blanco, J. / SanMartin, C.
Citation
Journal: Sci Adv / Year: 2021
Title: Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins.
Authors: Roberto Marabini / Gabriela N Condezo / Mart Krupovic / Rosa Menéndez-Conejero / Josué Gómez-Blanco / Carmen San Martín /
Abstract: Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with ...Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with nonmammalian host: lizard atadenovirus LAdV-2. We find a large conformational difference in the internal vertex protein IIIa between mast- and atadenoviruses, induced by the presence of an extended polypeptide. This polypeptide, and α-helical clusters beneath the facet, likely correspond to genus-specific proteins LH2 and p32k. Another genus-specific protein, LH3, with a fold typical of bacteriophage tailspikes, contacts the capsid surface via a triskelion structure identical to that used by mastadenovirus protein IX, revealing a conserved capsid-binding motif and an ancient gene duplication event. Our data also suggest that mastadenovirus E1B-55 K was exapted from the atadenovirus-like LH3 protein. This work provides new information on the evolution of adenoviruses, emphasizing the importance of minor coat proteins for determining specific physicochemical properties of virions and most likely their tropism.
#1: Journal: Biorxiv / Year: 2020
Title: Near Atomic Structure of an Atadenovirus Reveals a Conserved Capsid-Binding Motif and Intergenera Variations in Cementing Proteins
Authors: Marabini, R. / Condezo, G.N. / Gomez-Blanco, J. / San Martin, C.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author

-
Structure visualization

Movie
  • Biological unit as author_and_software_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4551
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4551
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hexon protein
L: Hexon protein
K: Hexon protein
J: Hexon protein
H: Hexon protein
I: Hexon protein
G: Hexon protein
F: Hexon protein
E: Hexon protein
D: Hexon protein
C: Hexon protein
B: Hexon protein
S: Protein LH3
T: Protein LH3
R: Protein LH3
Q: Protein LH3
P: Pre-hexon-linking protein VIII
O: Pre-hexon-linking protein VIII
N: PIIIa
M: Penton protein


Theoretical massNumber of molelcules
Total (without water)1,566,13520
Polymers1,566,13520
Non-polymers00
Water0
1
A: Hexon protein
L: Hexon protein
K: Hexon protein
J: Hexon protein
H: Hexon protein
I: Hexon protein
G: Hexon protein
F: Hexon protein
E: Hexon protein
D: Hexon protein
C: Hexon protein
B: Hexon protein
S: Protein LH3
T: Protein LH3
R: Protein LH3
Q: Protein LH3
P: Pre-hexon-linking protein VIII
O: Pre-hexon-linking protein VIII
N: PIIIa
M: Penton protein
x 60


Theoretical massNumber of molelcules
Total (without water)93,968,0731200
Polymers93,968,0731200
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59
MethodPISA
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
Hexon protein / / CP-H / Protein II


Mass: 101861.930 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Lizard adenovirus 2 / References: UniProt: A0A076FYV7
#2: Protein
Protein LH3


Mass: 41158.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Lizard adenovirus 2 / References: UniProt: A0A076FYU8
#3: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 30744.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lizard adenovirus 2 / References: UniProt: A0A076FT36
#4: Protein PIIIa


Mass: 67049.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lizard adenovirus 2 / References: UniProt: A0A076FYV2
#5: Protein Penton protein / / CP-P / Penton base protein / Protein III


Mass: 50619.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lizard adenovirus 2 / References: UniProt: A0A076FT28

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Lizard adenovirus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 150 MDa / Experimental value: NO
Source (natural)Organism: Lizard adenovirus 2
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Heloderma horridum
Virus shellDiameter: 940 nm / Triangulation number (T number): 25
Buffer solutionpH: 7.4 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Quantifoil R2/4
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 2 sec. / Electron dose: 54 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
EM software
IDNameCategory
2Scipionparticle selection
5CTFFINDCTF correction
6ScipionCTF correction
9UCSF Chimeramodel fitting
10Scipionmodel fitting
12RELIONinitial Euler assignment
13Scipioninitial Euler assignment
14RELIONfinal Euler assignment
15Scipionfinal Euler assignment
16RELIONclassification
17Scipionclassification
18RELION3D reconstruction
19Scipion3D reconstruction
20Cootmodel refinement
21PHENIXmodel refinement
22REFMACmodel refinement
23Scipionmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16071 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064108998
ELECTRON MICROSCOPYf_angle_d0.9774148862
ELECTRON MICROSCOPYf_chiral_restr0.0615835
ELECTRON MICROSCOPYf_plane_restr0.007319857
ELECTRON MICROSCOPYf_dihedral_angle_d6.784363967

+
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