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- PDB-2d31: Crystal structure of disulfide-linked HLA-G dimer -

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Basic information

Entry
Database: PDB / ID: 2d31
TitleCrystal structure of disulfide-linked HLA-G dimer
Components
  • 9-mer peptide from Histone H2A
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain G
KeywordsIMMUNE SYSTEM/CELL CYCLE / MHC class I / IMMUNE SYSTEM-CELL CYCLE COMPLEX
Function / homology
Function and homology information


peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / positive regulation of natural killer cell cytokine production / positive regulation of T cell tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of T cell mediated cytotoxicity / negative regulation of immune response / negative regulation of G0 to G1 transition / cis-Golgi network membrane ...peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / positive regulation of natural killer cell cytokine production / positive regulation of T cell tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of T cell mediated cytotoxicity / negative regulation of immune response / negative regulation of G0 to G1 transition / cis-Golgi network membrane / positive regulation of macrophage cytokine production / protein localization to site of double-strand break / negative regulation of natural killer cell mediated cytotoxicity / XY body / filopodium membrane / chromatin-protein adaptor activity / positive regulation of regulatory T cell differentiation / response to ionizing radiation / protein homotrimerization / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / positive regulation of endothelial cell apoptotic process / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of interleukin-12 production / cellular defense response / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / DNA damage checkpoint signaling / male germ cell nucleus / Regulation of PD-L1(CD274) transcription / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of angiogenesis / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Meiotic synapsis / T cell mediated cytotoxicity / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / condensed nuclear chromosome / Endosomal/Vacuolar pathway / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / replication fork / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Defective pyroptosis / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / Formation of the beta-catenin:TCF transactivating complex / meiotic cell cycle / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / MHC class I protein complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / multicellular organismal-level iron ion homeostasis / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Histone H2A conserved site / Histone H2A signature. ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / MHC classes I/II-like antigen recognition protein / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Histone H2AX / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsShiroishi, M. / Kuroki, K. / Ose, T. / Rasubala, L. / Shiratori, I. / Arase, H. / Tsumoto, K. / Kumagai, I. / Kohda, D. / Maenaka, K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Efficient Leukocyte Ig-like Receptor Signaling and Crystal Structure of Disulfide-linked HLA-G Dimer
Authors: Shiroishi, M. / Kuroki, K. / Ose, T. / Rasubala, L. / Shiratori, I. / Arase, H. / Tsumoto, K. / Kumagai, I. / Kohda, D. / Maenaka, K.
History
DepositionSep 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 19, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.5Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: 9-mer peptide from Histone H2A
D: HLA class I histocompatibility antigen, alpha chain G
E: Beta-2-microglobulin
F: 9-mer peptide from Histone H2A


Theoretical massNumber of molelcules
Total (without water)89,8606
Polymers89,8606
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: 9-mer peptide from Histone H2A


Theoretical massNumber of molelcules
Total (without water)44,9303
Polymers44,9303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-17 kcal/mol
Surface area18960 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, alpha chain G
E: Beta-2-microglobulin
F: 9-mer peptide from Histone H2A


Theoretical massNumber of molelcules
Total (without water)44,9303
Polymers44,9303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-20 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.641, 127.807, 72.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HLA class I histocompatibility antigen, alpha chain G / HLA G antigen / HLA heavy chain


Mass: 31902.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17693
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide 9-mer peptide from Histone H2A


Mass: 1148.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104
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: 2.5 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: CAPS, PEG8000, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 12897 / % possible obs: 83.8 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1162 / % possible all: 77.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHE

1mhe


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.799 / SU B: 30.757 / SU ML: 0.526 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29835 896 7.1 %RANDOM
Rwork0.2347 ---
obs0.2394 11791 83.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.62 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6124 0 0 0 6124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216293
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9358532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90623.304342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.671151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2421559
X-RAY DIFFRACTIONr_chiral_restr0.0940.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024961
X-RAY DIFFRACTIONr_nbd_refined0.2440.23058
X-RAY DIFFRACTIONr_nbtor_refined0.310.24120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.26
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 73 -
Rwork0.272 844 -
obs--83.82 %

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