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- PDB-4myv: Free HSV-2 gD structure -

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Basic information

Entry
Database: PDB / ID: 4myv
TitleFree HSV-2 gD structure
ComponentsEnvelope glycoprotein D
KeywordsVIRAL PROTEIN / IgV-like core / N-/C-terminal extensions / receptor binding / nectin-1 / HVEM / viral surface
Function / homology
Function and homology information


coreceptor-mediated virion attachment to host cell / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Distorted Sandwich / Immunoglobulin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein D
Similarity search - Component
Biological speciesHuman herpesvirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 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 1.3Nov 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: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4314
Polymers65,9892
Non-polymers4422
Water7,332407
1
A: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2162
Polymers32,9941
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2162
Polymers32,9941
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.562, 55.351, 65.335
Angle α, β, γ (deg.)90.00, 96.35, 90.00
Int Tables number4
Space group name H-MP1211

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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: 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 / N-Acetylglucosamine


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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1mol/L Hepes pH 7.2, 5% (V/V) MPD, 10% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 41946 / Num. obs: 40614 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 15.89
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.714 / Num. unique all: 3384 / Rsym value: 0.297 / % possible all: 81.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L2G

1l2g


Resolution: 1.801→36.268 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 2038 5.02 %Random
Rwork0.1886 ---
obs0.1907 40596 96.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→36.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 28 407 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082920
X-RAY DIFFRACTIONf_angle_d1.3153986
X-RAY DIFFRACTIONf_dihedral_angle_d16.6811067
X-RAY DIFFRACTIONf_chiral_restr0.094447
X-RAY DIFFRACTIONf_plane_restr0.005507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8012-1.84310.33431090.2601206778
1.8431-1.88920.27311340.2281230288
1.8892-1.94030.20481240.1964246693
1.9403-1.99740.20121430.189256596
1.9974-2.06180.24241370.1866256298
2.0618-2.13550.23061400.1967260499
2.1355-2.2210.21051260.19392640100
2.221-2.32210.27891370.18852653100
2.3221-2.44450.27111370.1912650100
2.4445-2.59760.231510.19652619100
2.5976-2.79810.23661200.19372666100
2.7981-3.07950.25831540.19182680100
3.0795-3.52480.19411460.18462650100
3.5248-4.43970.21491410.16722693100
4.4397-36.27520.21671390.18452741100

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