[English] 日本語
Yorodumi
- PDB-6tm8: Crystal structure of glycoprotein D of Equine Herpesvirus Type 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tm8
TitleCrystal structure of glycoprotein D of Equine Herpesvirus Type 4
ComponentsEnvelope glycoprotein D
KeywordsVIRAL PROTEIN / glycoprotein D / equine herpesvirus type 4 / EHV-4 / viral entry
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Immunoglobulin-like domain superfamily / viral envelope / membrane / Envelope glycoprotein D
Function and homology information
Biological speciesEquid alphaherpesvirus 4 (Equine herpesvirus 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKremling, V. / Loll, B. / Osterrieder, N. / Wahl, M. / Dahmani, I. / Chiantia, P. / Azab, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Front Microbiol / Year: 2023
Title: Crystal structures of glycoprotein D of equine alphaherpesviruses reveal potential binding sites to the entry receptor MHC-I.
Authors: Kremling, V. / Loll, B. / Pach, S. / Dahmani, I. / Weise, C. / Wolber, G. / Chiantia, S. / Wahl, M.C. / Osterrieder, N. / Azab, W.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3925
Polymers38,0241
Non-polymers3684
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-1 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.095, 59.554, 69.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Envelope glycoprotein D


Mass: 38023.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equid alphaherpesvirus 4 (Equine herpesvirus 4)
Gene: ORF72 / Plasmid: pMultiBac / Cell line (production host): H5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0A4Z5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM MgCl2, 100 mM MES pH 6.5, 30% (w/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 23671 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.174 / Net I/σ(I): 8.96
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.5 % / Num. unique obs: 10835 / CC1/2: 0.409 / Rrim(I) all: 1.268 / % possible all: 78.2

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SQJ

6sqj


Resolution: 1.9→46.17 Å / SU ML: 0.2323 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.9286
RfactorNum. reflection% reflection
Rfree0.2131 1181 5 %
Rwork0.1747 --
obs0.1766 23641 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 24 174 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182116
X-RAY DIFFRACTIONf_angle_d1.04842882
X-RAY DIFFRACTIONf_chiral_restr0.0724312
X-RAY DIFFRACTIONf_plane_restr0.0062376
X-RAY DIFFRACTIONf_dihedral_angle_d15.70341281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.36221150.2892209X-RAY DIFFRACTION76.1
1.98-2.090.25911380.2392610X-RAY DIFFRACTION90.96
2.09-2.220.24721510.21382885X-RAY DIFFRACTION99.41
2.22-2.390.24611520.18742898X-RAY DIFFRACTION99.87
2.39-2.630.22381520.18572890X-RAY DIFFRACTION99.54
2.63-3.010.21221540.17052928X-RAY DIFFRACTION99.68
3.01-3.790.20411560.15092959X-RAY DIFFRACTION99.71
3.79-46.170.17071630.15243081X-RAY DIFFRACTION99.42
Refinement TLS params.Method: refined / Origin x: -18.3823856533 Å / Origin y: -2.65350132849 Å / Origin z: 8.15552908134 Å
111213212223313233
T0.187538718025 Å2-0.00716998000124 Å2-0.0174305586347 Å2-0.19181688238 Å2-0.00774676326183 Å2--0.175914811394 Å2
L1.08303448248 °2-0.271478573776 °2-0.56564048638 °2-0.883928083347 °20.112895920261 °2--1.51176230378 °2
S0.00888018239749 Å °-0.0358414703727 Å °0.0771489708006 Å °0.0378010810245 Å °0.0388934891896 Å °-0.0704737126119 Å °-0.0126606984911 Å °0.076896253245 Å °-0.0440381811389 Å °
Refinement TLS groupSelection details: all

+
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