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- PDB-5xo2: Crystal structure of human paired immunoglobulin-like type 2 rece... -

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Basic information

Entry
Database: PDB / ID: 5xo2
TitleCrystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II
Components
  • Paired immunoglobulin-like type 2 receptor alpha
  • Peptide from Envelope glycoprotein B
KeywordsIMMUNE SYSTEM / membrane protein / immune receptor / viral entry inhibitor / glycopeptide
Function / homology
Function and homology information


MHC class I protein binding / host cell Golgi membrane / host cell endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / signal transduction ...MHC class I protein binding / host cell Golgi membrane / host cell endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral envelope / symbiont entry into host cell / 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
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: 2.201 Å
AuthorsFurukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. ...Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / Anada, M. / Ose, T. / Hashimoto, S. / Maenaka, K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and thermodynamic analyses reveal critical features of glycopeptide recognition by the human PILR alpha immune cell receptor.
Authors: Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / ...Authors: Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / Anada, M. / Ose, T. / Hashimoto, S. / Maenaka, K.
History
DepositionMay 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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 / 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_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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired immunoglobulin-like type 2 receptor alpha
B: Paired immunoglobulin-like type 2 receptor alpha
X: Peptide from Envelope glycoprotein B
Y: Peptide from Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1486
Polymers29,1554
Non-polymers9932
Water88349
1
A: Paired immunoglobulin-like type 2 receptor alpha
X: Peptide from Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0743
Polymers14,5772
Non-polymers4961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area6970 Å2
MethodPISA
2
B: Paired immunoglobulin-like type 2 receptor alpha
Y: Peptide from Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0743
Polymers14,5772
Non-polymers4961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-5 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.280, 63.329, 55.072
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Paired immunoglobulin-like type 2 receptor alpha / Cell surface receptor FDF03 / Inhibitory receptor PILR-alpha


Mass: 13967.697 Da / Num. of mol.: 2 / Fragment: UNP residues 32-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PILRA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKJ1
#2: Protein/peptide Peptide from Envelope glycoprotein B / gB


Mass: 609.671 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: P06437
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2,4-dideoxy-alpha-D-xylo-hexopyranose


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a21d2h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][D-1,4-deoxy-GlcpNAc]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13393 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 25
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.4 / Num. unique all: 668 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WV0

3wv0


Resolution: 2.201→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2616 638 -
Rwork0.2163 --
obs0.2286 13390 99.8 %
Refinement stepCycle: LAST / Resolution: 2.201→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 66 49 2173
LS refinement shellResolution: 2.201→2.279 Å /
RfactorNum. reflection
Rfree0.3188 -
Rwork0.2352 -
obs-673

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