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- PDB-3u82: Binding of herpes simplex virus glycoprotein D to nectin-1 exploi... -

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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 / Adherens junctions interactions / virion binding / apical junction complex ...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 / Adherens junctions interactions / virion binding / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / coreceptor activity / presynaptic active zone membrane / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / adherens junction / axon guidance / cell-cell adhesion / virus receptor activity / retina development in camera-type eye / iron ion transport / carbohydrate binding / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / cell adhesion / symbiont entry into host cell / immune response / viral envelope / dendrite / protein-containing complex binding / virion membrane / protein homodimerization activity / extracellular region / membrane / identical protein binding / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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