[English] 日本語
Yorodumi
- PDB-3u82: Binding of herpes simplex virus glycoprotein D to nectin-1 exploi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u82
TitleBinding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion
Components
  • Envelope glycoprotein D
  • Poliovirus receptor-related protein 1
KeywordsVIRAL PROTEIN/CELL ADHESION / HSV-1 gD / nectin-1 / binding mode / nectin-1 dimerization preclusion / VIRAL PROTEIN-CELL ADHESION complex
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / cell-cell contact zone / virion binding / Adherens junctions interactions / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / cell-cell contact zone / virion binding / Adherens junctions interactions / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / apical junction complex / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / coreceptor activity / cell adhesion molecule binding / presynaptic active zone membrane / hippocampal mossy fiber to CA3 synapse / axon guidance / adherens junction / cell-cell adhesion / retina development in camera-type eye / virus receptor activity / iron ion transport / carbohydrate binding / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / cell adhesion / immune response / symbiont entry into host cell / viral envelope / dendrite / protein-containing complex binding / virion membrane / protein homodimerization activity / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain ...Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Distorted Sandwich / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nectin-1 / Envelope glycoprotein D
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.164 Å
AuthorsZhang, N. / Yan, J. / Lu, G. / Guo, Z. / Fan, Z. / Wang, J. / Shi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2011
Title: Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion.
Authors: Zhang, N. / Yan, J. / Lu, G. / Guo, Z. / Fan, Z. / Wang, J. / Shi, Y. / Qi, J. / Gao, G.F.
History
DepositionOct 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein D
B: Poliovirus receptor-related protein 1


Theoretical massNumber of molelcules
Total (without water)67,9712
Polymers67,9712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-10 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.532, 169.043, 183.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Envelope glycoprotein D / gD


Mass: 32481.893 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: 17 / Gene: gD, US6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q69091
#2: Protein Poliovirus receptor-related protein 1 / Herpes virus entry mediator C / Herpesvirus entry mediator C / HveC / Herpesvirus Ig-like receptor ...Herpes virus entry mediator C / Herpesvirus entry mediator C / HveC / Herpesvirus Ig-like receptor / HIgR / Nectin-1


Mass: 35488.844 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRL1, HVEC, PRR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15223

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 1000, 0.1M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dehydrate, pH 5.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3.164→50 Å / Num. all: 13572 / Num. obs: 13572 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1158 / % possible all: 82.7

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C36, 3ALP

2c36

3alp


Resolution: 3.164→38.378 Å / SU ML: 0.5 / σ(F): 0.04 / Phase error: 43.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3443 564 4.79 %RANDOM
Rwork0.321 ---
all0.3223 11786 --
obs0.3223 11786 81.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 130.701 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-108.2346 Å2-0 Å2-0 Å2
2---63.8161 Å20 Å2
3----44.4185 Å2
Refinement stepCycle: LAST / Resolution: 3.164→38.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 0 4164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014292
X-RAY DIFFRACTIONf_angle_d1.3435850
X-RAY DIFFRACTIONf_dihedral_angle_d19.8821555
X-RAY DIFFRACTIONf_chiral_restr0.085650
X-RAY DIFFRACTIONf_plane_restr0.005763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1644-3.48270.5191180.4611215864
3.4827-3.98620.3871530.3771278082
3.9862-5.02040.29091430.2875298588
5.0204-38.38070.32661500.2992329992

+
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