[English] 日本語
Yorodumi
- PDB-3wv0: O-glycan attached to herpes simplex virus type 1 glycoprotein gB ... -

+
Open data


ID or keywords:

Loading...

-
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 ...: / : / 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more