[English] 日本語
Yorodumi
- PDB-3d2u: Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a ... -

+
Open data


ID or keywords:

Loading...

-
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-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


symbiont-mediated perturbation of host natural killer cell mediated immune response / HLA-A specific inhibitory MHC class I receptor activity / : / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway ...symbiont-mediated perturbation of host natural killer cell mediated immune response / HLA-A specific inhibitory MHC class I receptor activity / : / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity / MHC class Ib protein binding / negative regulation of T cell mediated cytotoxicity / negative regulation of CD8-positive, alpha-beta T cell activation / immune response-regulating signaling pathway / negative regulation of transforming growth factor beta production / MHC class I receptor activity / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / positive regulation of norepinephrine uptake / dendritic cell differentiation / interleukin-10-mediated signaling pathway / negative regulation of osteoclast development / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of interleukin-12 production / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / cellular response to cytochalasin B / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / negative regulation of dendritic cell apoptotic process / regulation of transepithelial transport / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / morphogenesis of a polarized epithelium / negative regulation of endocytosis / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Formation of the non-canonical BAF (ncBAF) complex / Gap junction degradation / GBAF complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / protein localization to adherens junction / dense body / Folding of actin by CCT/TriC / negative regulation of interferon-beta production / Tat protein binding / postsynaptic actin cytoskeleton / negative regulation of mononuclear cell proliferation / RSC-type complex / negative regulation of natural killer cell mediated cytotoxicity / Regulation of CDH1 Function / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / RHOF GTPase cycle / T cell proliferation involved in immune response / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / positive regulation of macrophage cytokine production / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / tight junction / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / negative regulation of interleukin-10 production / apical junction complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / negative regulation of type II interferon production / Regulation of MITF-M-dependent genes involved in pigmentation / cortical cytoskeleton / Recycling pathway of L1 / negative regulation of calcium ion transport / negative regulation of cell cycle / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / brush border / MHC class I protein binding / EPH-ephrin mediated repulsion of cells / negative regulation of tumor necrosis factor production / host cell membrane / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / kinesin binding
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 ...: / 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 / MHC classes I/II-like antigen recognition protein / : / ATPase, nucleotide binding domain / 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein , 2 types, 4 molecules BFDH

#2: Protein 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

-
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


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

-
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


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


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


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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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