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- PDB-3d2u: Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a ... -

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Basic information

Entry
Database: PDB / ID: 3d2u
TitleStructure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor
Components
  • Actin
  • Beta-2-microglobulinBeta-2 microglobulin
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • UL18 protein
KeywordsIMMUNE SYSTEM / MHC class I homolog / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted / Membrane / Phosphoprotein / Receptor / Transmembrane
Function / homology
Function and homology information


evasion by virus of host natural killer cell activity / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway ...evasion by virus of host natural killer cell activity / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation / MHC class Ib receptor activity / positive regulation of norepinephrine uptake / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / cellular response to cytochalasin B / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / bBAF complex / negative regulation of serotonin secretion / negative regulation of cytokine production involved in immune response / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / dendritic cell differentiation / morphogenesis of a polarized epithelium / GBAF complex / postsynaptic actin cytoskeleton / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein localization to adherens junction / protein phosphatase 1 binding / Formation of annular gap junctions / regulation of G0 to G1 transition / dense body / Gap junction degradation / Tat protein binding / negative regulation of osteoclast development / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of double-strand break repair / negative regulation of interleukin-12 production / regulation of nucleotide-excision repair / negative regulation of endocytosis / RSC-type complex / apical protein localization / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of macrophage cytokine production / T cell proliferation involved in immune response / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / negative regulation of natural killer cell mediated cytotoxicity / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / negative regulation of interleukin-10 production / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / cortical cytoskeleton / nitric-oxide synthase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / brush border / calyx of Held / kinesin binding / negative regulation of calcium ion transport / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cell cycle / EPH-ephrin mediated repulsion of cells / host cell membrane / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / MHC class I protein binding / regulation of protein localization to plasma membrane / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / EPHB-mediated forward signaling / substantia nigra development
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / ATPase, nucleotide binding domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-L-fucopyranose / alpha-D-mannopyranose / Glycoprotein UL18 / Actin, cytoplasmic 1 / Beta-2-microglobulin / Membrane glycoprotein UL18 / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHuman herpesvirus 5
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsYang, Z. / Bjorkman, P.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor
Authors: Yang, Z. / Bjorkman, P.J.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / refine / struct_ref_seq_dif
Item: _chem_comp.type / _entity.pdbx_mutation ..._chem_comp.type / _entity.pdbx_mutation / _pdbx_entity_src_syn.details / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.pdbx_R_Free_selection_details / _struct_ref_seq_dif.details
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: UL18 protein
B: Beta-2-microglobulin
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
E: UL18 protein
F: Beta-2-microglobulin
H: Leukocyte immunoglobulin-like receptor subfamily B member 1
G: Actin
C: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,34824
Polymers132,9488
Non-polymers3,40016
Water6,521362
1
A: UL18 protein
B: Beta-2-microglobulin
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
C: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,54714
Polymers66,4744
Non-polymers2,07310
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-19 kcal/mol
Surface area27330 Å2
MethodPISA
2
E: UL18 protein
F: Beta-2-microglobulin
H: Leukocyte immunoglobulin-like receptor subfamily B member 1
G: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,80110
Polymers66,4744
Non-polymers1,3276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-17 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.366, 98.110, 172.147
Angle α, β, γ (deg.)90.000, 98.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules BFDH

#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: beta2m / Source: (natural) Homo sapiens (human) / References: UniProt: P61769
#3: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1 / Leukocyte immunoglobulin-like receptor 1 / LIR-1 / Immunoglobulin- like transcript 2 / ILT-2 / ...Leukocyte immunoglobulin-like receptor 1 / LIR-1 / Immunoglobulin- like transcript 2 / ILT-2 / Monocyte/macrophage immunoglobulin-like receptor 7 / MIR-7 / CD85j antigen


Mass: 22055.697 Da / Num. of mol.: 2 / Fragment: Ig-like C2-type 1 and C2-type 2 domains / Source method: isolated from a natural source / Details: LIR-1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NHL6

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Antibody / Protein/peptide / Non-polymers , 3 types, 366 molecules AEGC

#1: Antibody UL18 protein


Mass: 31664.994 Da / Num. of mol.: 2 / Fragment: sequence database residues 21-301 / Source method: isolated from a natural source / Details: gene UL18 / Source: (natural) Human herpesvirus 5 / Strain: AD169 / References: UniProt: Q4A1U8, UniProt: P08560*PLUS
#4: Protein/peptide Actin /


Mass: 1005.257 Da / Num. of mol.: 2 / Fragment: sequence database residues 170-178 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 16 molecules

#5: 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.: 13
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
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 85873 / % possible obs: 98.6 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.6 / Num. unique all: 7747 / % possible all: 89.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P7Q

1p7q


Resolution: 2.21→47.46 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4149 -RANDOM
Rwork0.241 ---
obs-85873 97 %-
Displacement parametersBiso mean: 42.508 Å2
Refine analyzeLuzzati coordinate error obs: 0.031 Å
Refinement stepCycle: LAST / Resolution: 2.21→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9089 0 230 362 9681
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7

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