[English] 日本語
Yorodumi
- PDB-7agf: HAd7 knob in complex with 3 EC2-EC3 modules of DSG-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7agf
TitleHAd7 knob in complex with 3 EC2-EC3 modules of DSG-2
Components
  • Desmoglein-2
  • Fiber
KeywordsVIRAL PROTEIN / adenovirus / cell receptor / complex
Function / homology
Function and homology information


Purkinje myocyte development / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / desmosome organization / cornified envelope / desmosome / regulation of ventricular cardiac muscle cell action potential / adhesion receptor-mediated virion attachment to host cell / cornification / regulation of heart rate by cardiac conduction ...Purkinje myocyte development / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / desmosome organization / cornified envelope / desmosome / regulation of ventricular cardiac muscle cell action potential / adhesion receptor-mediated virion attachment to host cell / cornification / regulation of heart rate by cardiac conduction / keratinization / intercalated disc / maternal process involved in female pregnancy / lateral plasma membrane / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / cell-cell adhesion / response to progesterone / viral capsid / cell junction / cell-cell junction / apical plasma membrane / viral entry into host cell / cell adhesion / intracellular membrane-bounded organelle / calcium ion binding / host cell nucleus / cell surface / extracellular exosome / integral component of membrane / plasma membrane / nucleus
Adenovirus fibre protein / Desmosomal cadherin / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Cadherin-like / Adenovirus pIV-like, attachment domain / Attachment protein shaft domain superfamily / Desmoglein / Cadherin-like superfamily / Cadherin conserved site / Catenin binding domain superfamily
Desmoglein-2 / Fiber
Biological speciesHuman adenovirus B serotype 7
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsEffantin, G. / Vassal-Stermann, E. / Fender, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0001 France
CitationJournal: Viruses / Year: 2020
Title: Binding Mechanism Elucidation of the Acute Respiratory Disease Causing Agent Adenovirus of Serotype 7 to Desmoglein-2.
Authors: Marc-André Hograindleur / Gregory Effantin / Daphna Fenel / Caroline Mas / André Lieber / Guy Schoehn / Pascal Fender / Emilie Vassal-Stermann /
Abstract: The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human ...The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human adenoviruses, adenovirus of serotype 7 (HAdV7) is one of the most virulent serotypes. This virus regularly re-emerges in Asia and has just been the cause of several deaths in the United States. A critical step of the virus life cycle is the attachment of the knob domain of the fiber (HAd7K) to the cellular receptor desmoglein-2 (DSG2). Complexes between the fiber knob and two extracellular domains of DSG2 have been produced. Their characterization by biochemical and biophysical methods show that these two domains are sufficient for the interaction and that the trimeric HAd7K could accommodate up to three DSG2 receptor molecules. The cryo-electron microscopy (cryo-EM) structure of these complexes at 3.1 Å resolution confirmed the biochemical data, and allowed the identification of the critical amino acid residues for this interaction, which shows similarities with other DSG2 interacting adenoviruses, despite a low homology in the primary sequences.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11778
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fiber
D: Desmoglein-2
E: Desmoglein-2
F: Desmoglein-2
B: Fiber
C: Fiber


Theoretical massNumber of molelcules
Total (without water)151,8466
Polymers151,8466
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_1ens_2chain "D"
d_2ens_2chain "E"
d_3ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPASPF1 - 198
d_21ens_1ASPASPE1 - 198
d_31ens_1ASPASPA1 - 198
d_11ens_2VALVALB1 - 231
d_21ens_2VALVALC1 - 231
d_31ens_2VALVALD1 - 231

NCS ensembles:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.500136271588, 0.865946709357, 7.99786116202E-5), (-0.8659465951, -0.500136153125, -0.000568130907481), (-0.000451970894669, -0.000353400080254, 0.999999835415)16.5014492447, 153.839616243, 0.0546696301126
2given(-0.499568205797, -0.866274553151, 7.94987289521E-5), (0.866274277552, -0.499567968969, 0.000848782932857), (-0.000695564037325, 0.000492892670867, 0.999999636624)141.457033235, 62.5692980224, 0.0156991767547
3given(-0.500775551654, -0.865577005667, 0.000542334305817), (0.865577033979, -0.500775729818, -0.000258210903232), (0.000495089278251, 0.000340126412345, 0.9999998196)141.455740462, 62.7469219639, -0.027285756196
4given(-0.498183090378, 0.867070852808, 0.00132086030597), (-0.867071794439, -0.498181887993, -0.00114444937255), (-0.000334290012446, -0.0017154260409, 0.999998472781)16.1832566801, 153.811041387, 0.193899438733

-
Components

#1: Protein Fiber / / Fiber protein / L5 fiber protein


Mass: 23489.217 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B serotype 7 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EY45
#2: Protein Desmoglein-2 / / Cadherin family member 5 / HDGC


Mass: 27126.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSG2, CDHF5 / Production host: Homo sapiens (human) / References: UniProt: Q14126

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human adenovirus type 7 knob in complex with 2 EC2 EC3 modules of DSG-2COMPLEX#1-#20MULTIPLE SOURCES
2Desmoglein-2COMPLEX#21RECOMBINANT
3FiberCOMPLEX#11RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Human adenovirus B serotype 710519
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58219 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.67 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610269
ELECTRON MICROSCOPYf_angle_d0.84614010
ELECTRON MICROSCOPYf_dihedral_angle_d6.5741365
ELECTRON MICROSCOPYf_chiral_restr0.0541653
ELECTRON MICROSCOPYf_plane_restr0.0051815
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefinement-IDTypeRms dev position (Å)
ens_1d_2FELECTRON MICROSCOPYNCS constraints0.000702045966641
ens_1d_3FELECTRON MICROSCOPYNCS constraints0.000714009299312
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.000708597483044
ens_2d_3BELECTRON MICROSCOPYNCS constraints0.000718493983979

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (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 PDBe / 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

Read more

-
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.

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