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- PDB-1ydp: 1.9A crystal structure of HLA-G -

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Basic information

Entry
Database: PDB / ID: 1ydp
Title1.9A crystal structure of HLA-G
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • histone 2a peptide
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell tolerance induction / XY body / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of regulatory T cell differentiation ...peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell tolerance induction / XY body / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of regulatory T cell differentiation / positive regulation of endothelial cell apoptotic process / filopodium membrane / positive regulation of natural killer cell cytokine production / cis-Golgi network membrane / positive regulation of macrophage cytokine production / negative regulation of natural killer cell mediated cytotoxicity / response to ionizing radiation / protein homotrimerization / site of DNA damage / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / CD8 receptor binding / cellular defense response / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of DNA repair / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / positive regulation of interleukin-12 production / Assembly of the ORC complex at the origin of replication / negative regulation of angiogenesis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / replication fork / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / meiotic cell cycle / PRC2 methylates histones and DNA / early endosome lumen / DNA damage checkpoint signaling / positive regulation of receptor binding / condensed nuclear chromosome / Nef mediated downregulation of MHC class I complex cell surface expression / male germ cell nucleus / DAP12 interactions / negative regulation of receptor binding / Defective pyroptosis / lumenal side of endoplasmic reticulum membrane / RNA Polymerase I Promoter Escape / Endosomal/Vacuolar pathway / Nonhomologous End-Joining (NHEJ) / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / cellular response to gamma radiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of forebrain neuron differentiation / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / ER to Golgi transport vesicle membrane / B-WICH complex positively regulates rRNA expression / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / DNA Damage/Telomere Stress Induced Senescence / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cerebral cortex development / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / RMTs methylate histone arginines / positive regulation of T cell cytokine production / Meiotic recombination / Pre-NOTCH Transcription and Translation / MHC class I protein complex / nucleosome assembly / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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/H2B/H3 / Core histone H2A/H2B/H3/H4 / MHC classes I/II-like antigen recognition protein / 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 / Immunoglobulins / Immunoglobulin-like fold / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsClements, C.S. / Kjer-nielsen, L. / Kostenko, L. / Hoare, H.L. / Dunstone, M.A. / Moses, E. / Freed, K. / Brooks, A.G. / Rossjohn, J. / Mccluskey, J.
CitationJournal: PROC.NATL.ACAD.SCI.USA / Year: 2005
Title: Crystal structure of HLA-G: A nonclassical MHC class I molecule expressed at the fetal-maternal interface
Authors: Clements, C.S. / Kjer-Nielsen, L. / Kostenko, L. / Hoare, H.L. / Dunstone, M.A. / Moses, E. / Freed, K. / Brooks, A.G. / Rossjohn, J. / McCluskey, J.
History
DepositionDec 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_entity_src_syn
Item: _entity.src_method / _pdbx_entity_src_syn.details ..._entity.src_method / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
P: histone 2a peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0166
Polymers44,8863
Non-polymers1303
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-33 kcal/mol
Surface area19070 Å2
MethodPISA
2
B: Beta-2-microglobulin
hetero molecules

A: MHC class I antigen
P: histone 2a peptide


Theoretical massNumber of molelcules
Total (without water)45,0166
Polymers44,8863
Non-polymers1303
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
Buried area3030 Å2
ΔGint-40 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.150, 77.150, 151.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31858.312 Da / Num. of mol.: 1 / Fragment: HLA-G heavy chain / Mutation: C42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P17693
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / HLA-G / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide histone 2a peptide


Mass: 1148.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P16104*PLUS

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Non-polymers , 3 types, 430 molecules

#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.62 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 130133

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å /
RfactorNum. reflection
Rfree0.264 -
Rwork0.235 -
obs-40820
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 3 427 3590

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