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- PDB-3wv0: O-glycan attached to herpes simplex virus type 1 glycoprotein gB ... -

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Basic information

Entry
Database: PDB / ID: 3wv0
TitleO-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha
Components
  • Envelope glycoprotein B
  • Paired immunoglobulin-like type 2 receptor alpha
KeywordsMEMBRANE PROTEIN / Immunoglobulin-like / Immunological receptor / Membrane
Function / homology
Function and homology information


MHC class I protein binding / host cell Golgi membrane / host cell endosome membrane / cell periphery / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane ...MHC class I protein binding / host cell Golgi membrane / host cell endosome membrane / cell periphery / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / 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
Paired immunoglobin like type 2 receptor alpha / Envelope glycoprotein B / Paired immunoglobulin-like type 2 receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKuroki, K. / Wang, J. / Ose, T. / Yamaguchi, M. / Tabata, S. / Maita, N. / Nakamura, S. / Kajikawa, M. / Kogure, A. / Satoh, T. ...Kuroki, K. / Wang, J. / Ose, T. / Yamaguchi, M. / Tabata, S. / Maita, N. / Nakamura, S. / Kajikawa, M. / Kogure, A. / Satoh, T. / Arase, H. / Maenaka, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for simultaneous recognition of an O-glycan and its attached peptide of mucin family by immune receptor PILR alpha
Authors: Kuroki, K. / Wang, J. / Ose, T. / Yamaguchi, M. / Tabata, S. / Maita, N. / Nakamura, S. / Kajikawa, M. / Kogure, A. / Satoh, T. / Arase, H. / Maenaka, K.
History
DepositionMay 10, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Paired immunoglobulin-like type 2 receptor alpha
B: Paired immunoglobulin-like type 2 receptor alpha
X: Envelope glycoprotein B
Y: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94814
Polymers29,1554
Non-polymers1,79310
Water2,918162
1
A: Paired immunoglobulin-like type 2 receptor alpha
X: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3786
Polymers14,5772
Non-polymers8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-6 kcal/mol
Surface area7360 Å2
MethodPISA
2
B: Paired immunoglobulin-like type 2 receptor alpha
Y: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5708
Polymers14,5772
Non-polymers9936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-5 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.313, 155.887, 67.354
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 Paired immunoglobulin-like type 2 receptor alpha


Mass: 13967.697 Da / Num. of mol.: 2 / Fragment: V-set domain, UNP residues 32-150 / Mutation: R78G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PILRA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9JGG1, UniProt: Q9UKJ1*PLUS
#2: Protein/peptide Envelope glycoprotein B / gB / gB-1 / gB1


Mass: 609.671 Da / Num. of mol.: 2
Fragment: O-glycan with attached peptide, UNP residues 50-56
Source method: obtained synthetically
Details: O-glycan with peptide derived from human herpesvirus 1
Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: P06437
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 512.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium sulfate 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12122 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 13.473 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.156 / Net I/σ(I): 4.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.512 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WUZ

3wuz


Resolution: 2.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 584 -RANDOM
Rwork0.231 ---
all-12150 --
obs-12109 99.7 %-
Displacement parametersBiso mean: 15.141 Å2
Baniso -1Baniso -2Baniso -3
1--1.534 Å20 Å2-0 Å2
2---6.261 Å2-0 Å2
3---7.795 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 108 162 2312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.3→2.46 Å
RfactorNum. reflection
Rfree0.4315 59
Rwork0.2796 -
obs-1039

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