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- PDB-6ls9: Crystal structure of bovine herpesvirus 1 glycoprotein D -

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Basic information

Entry
Database: PDB / ID: 6ls9
TitleCrystal structure of bovine herpesvirus 1 glycoprotein D
ComponentsEnvelope glycoprotein D
KeywordsVIRAL PROTEIN / receptor recognition
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / membrane => GO:0016020 / Immunoglobulin-like domain superfamily / viral envelope / triacetyl-beta-chitotriose / Envelope glycoprotein D
Function and homology information
Biological speciesBovine alphaherpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsYue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. ...Yue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z.L. / You, Y. / Sun, H.L. / Wen, A. / Wang, L.L. / Zheng, Y. / Cao, Y. / Li, Y.H. / Lu, G.W.
CitationJournal: Sci Adv / Year: 2020
Title: Crystal structure of bovine herpesvirus 1 glycoprotein D bound to nectin-1 reveals the basis for its low-affinity binding to the receptor.
Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / ...Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / Cao, Y. / Li, Y. / Lu, G.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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 / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein D
B: Envelope glycoprotein D
C: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9067
Polymers104,6153
Non-polymers1,2914
Water1,24369
1
A: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7203
Polymers34,8721
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0932
Polymers34,8721
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Envelope glycoprotein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0932
Polymers34,8721
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.272, 104.392, 98.772
Angle α, β, γ (deg.)90.000, 112.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Envelope glycoprotein D / Glycoprotein D


Mass: 34871.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine alphaherpesvirus 1
Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_ ...Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_00067, OHMFJBFK_00067
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q76PF1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: 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.: 3
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Ammonium acetate, 0.1M Tris-HCl, 16% w/v Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03645 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03645 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 37572 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.111
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.573 / Num. unique obs: 3702

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5V

5x5v


Resolution: 2.503→37.433 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1848 4.92 %
Rwork0.2053 35717 -
obs0.2072 37565 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.84 Å2 / Biso mean: 37.4004 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: final / Resolution: 2.503→37.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5883 0 84 69 6036
Biso mean--65.62 31.66 -
Num. residues----721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126198
X-RAY DIFFRACTIONf_angle_d1.2058477
X-RAY DIFFRACTIONf_chiral_restr0.08859
X-RAY DIFFRACTIONf_plane_restr0.0081085
X-RAY DIFFRACTIONf_dihedral_angle_d19.9293617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.503-2.57040.38351330.2932268597
2.5704-2.6460.31621490.28052698100
2.646-2.73140.30871320.27182761100
2.7314-2.8290.31881230.25452767100
2.829-2.94220.30121440.24652718100
2.9422-3.07610.2521330.25032764100
3.0761-3.23820.3021450.24042762100
3.2382-3.44090.27771380.22882742100
3.4409-3.70640.24841720.20122730100
3.7064-4.0790.23221360.19042744100
4.079-4.66820.17381490.15062762100
4.6682-5.87780.20831390.1582778100
5.8778-37.4330.21191550.19692806100

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