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- PDB-4myw: Structure of HSV-2 gD bound to nectin-1 -

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Basic information

Entry
Database: PDB / ID: 4myw
TitleStructure of HSV-2 gD bound to nectin-1
Components
  • Envelope glycoprotein D
  • Poliovirus receptor-related protein 1
KeywordsVIRAL PROTEIN/CELL ADHESION / IgV-like core / N-/C-terminal extensions / tandem arranged V-C-C Ig-like domains / receptor binding / cell surface attachment / viral / cellular surface / VIRAL PROTEIN-CELL ADHESION complex
Function / homology
Function and homology information


coreceptor-mediated virion attachment to host cell / 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 ...coreceptor-mediated virion attachment to host cell / 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 / retina development in camera-type eye / virus receptor activity / iron ion transport / carbohydrate binding / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / immune response / fusion of virus membrane with host plasma membrane / 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 subtype 2 ...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 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
Envelope glycoprotein D / Nectin-1
Similarity search - Component
Biological speciesHuman herpesvirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.189 Å
AuthorsLu, G. / Zhang, N. / Qi, J. / Li, Y. / Chen, Z. / Zheng, C. / Yan, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2014
Title: Crystal structure of herpes simplex virus 2 gD bound to nectin-1 reveals a conserved mode of receptor recognition.
Authors: Lu, G. / Zhang, N. / Qi, J. / Li, Y. / Chen, Z. / Zheng, C. / Gao, G.F. / Yan, J.
History
DepositionSep 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,1578
Polymers139,8664
Non-polymers1,2914
Water1,02757
1
A: Envelope glycoprotein D
B: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5794
Polymers69,9332
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-4 kcal/mol
Surface area27410 Å2
MethodPISA
2
C: Envelope glycoprotein D
D: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5794
Polymers69,9332
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-6 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.337, 170.857, 192.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Envelope glycoprotein D / gD


Mass: 32994.465 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Strain: 333 / Gene: gD, US6 / Plasmid: pFast-bac1 / Cell (production host): High5 / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03172
#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: 36938.492 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVEC, nectin-1, PRR1, PVRL1 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15223
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL VARIANT AT THIS POSITION. THE SEQUENCE IS BASED ON A RECORD IN GENBANK WITH THE ACCESSION ...NATURAL VARIANT AT THIS POSITION. THE SEQUENCE IS BASED ON A RECORD IN GENBANK WITH THE ACCESSION NUMBER EU018091

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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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M sodium chloride, 0.1M sodium cacodylate, 8% w/v PEG 8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 3.189→50 Å / Num. all: 30221 / Num. obs: 30129 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 15.672
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.884 / Num. unique all: 2969 / Rsym value: 0.492 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U82

3u82


Resolution: 3.189→38.93 Å / SU ML: 0.29 / σ(F): 0.13 / Phase error: 24.55 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1451 5.04 %Random
Rwork0.1955 ---
obs0.1981 28799 95.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.088 Å2 / ksol: 0.294 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.5639 Å2-0 Å2-0 Å2
2---12.6572 Å20 Å2
3----8.9067 Å2
Refinement stepCycle: LAST / Resolution: 3.189→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8432 0 84 57 8573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058752
X-RAY DIFFRACTIONf_angle_d0.92411934
X-RAY DIFFRACTIONf_dihedral_angle_d21.1983196
X-RAY DIFFRACTIONf_chiral_restr0.0571346
X-RAY DIFFRACTIONf_plane_restr0.0041536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1894-3.30330.31711330.2716234684
3.3033-3.43550.32221220.2601258391
3.4355-3.59170.29971330.2362265693
3.5917-3.7810.31191500.2177268396
3.781-4.01760.24691310.1974274996
4.0176-4.32750.26711300.1786279798
4.3275-4.76230.19721620.1492280098
4.7623-5.44980.2111910.151281199
5.4498-6.860.24441510.183289199
6.86-38.93320.20981480.1823303298
Refinement TLS params.Method: refined / Origin x: -30.84 Å / Origin y: 41.4651 Å / Origin z: -7.6333 Å
111213212223313233
T0.3801 Å20.0084 Å2-0.0095 Å2-0.3636 Å2-0.0257 Å2--0.3578 Å2
L0.0351 °20.0611 °20.0469 °2-0.2311 °20.2204 °2--0.1571 °2
S-0.0009 Å °-0.0095 Å °-0.0203 Å °0.0668 Å °0.001 Å °-0.0389 Å °0.0672 Å °-0.0436 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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