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- PDB-3kyn: Crystal structure of HLA-G presenting KGPPAALTL peptide -

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Basic information

Entry
Database: PDB / ID: 3kyn
TitleCrystal structure of HLA-G presenting KGPPAALTL peptide
Components
  • Beta-2-microglobulin
  • KGPPAALTL peptide
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Human leukocyte antigen / major histocompatibility complex / immune response / MHC I
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 / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of G0 to G1 transition ...peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of endothelial cell apoptotic process / positive regulation of regulatory T cell differentiation / filopodium membrane / positive regulation of macrophage cytokine production / CD8 receptor binding / protein homotrimerization / protection from natural killer cell mediated cytotoxicity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular defense response / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / negative regulation of angiogenesis / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / early endosome / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum
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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins 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 / MHC classes I/II-like antigen recognition protein / 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
: / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalpole, N.G. / Rossjohn, J. / Clements, C.S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The structure and stability of the monomorphic HLA-G are influenced by the nature of the bound peptide
Authors: Walpole, N.G. / Kjer-Nielsen, L. / Kostenko, L. / McCluskey, J. / Brooks, A.G. / Rossjohn, J. / Clements, C.S.
History
DepositionDec 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,7396
Polymers44,6093
Non-polymers1303
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-18 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.874, 76.874, 151.851
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen / HLA-G


Mass: 31861.379 Da / Num. of mol.: 1 / Fragment: residues in UNP 26-299 / Mutation: C66S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-G / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: Q9MYA2, UniProt: P17693*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide KGPPAALTL peptide


Mass: 868.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide

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Non-polymers , 3 types, 116 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


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


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 18% PEG 3350, 0.2M potassium formate, 0.1M HEPES, 10mM cobalt chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→37.3 Å / Num. obs: 20378 / Biso Wilson estimate: 38.01 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDP

1ydp


Resolution: 2.4→37.27 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.134 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29913 1045 5.1 %RANDOM
Rwork0.21689 ---
obs0.22089 19333 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 3 113 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213226
X-RAY DIFFRACTIONr_bond_other_d0.0010.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9384377
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0025377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67523.372172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59515532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1311529
X-RAY DIFFRACTIONr_chiral_restr0.0910.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
X-RAY DIFFRACTIONr_nbd_refined0.2010.2612
X-RAY DIFFRACTIONr_nbd_other0.2010.22297
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21465
X-RAY DIFFRACTIONr_nbtor_other0.0860.21805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2126
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.29
X-RAY DIFFRACTIONr_mcbond_it1.91532488
X-RAY DIFFRACTIONr_mcbond_other0.3413766
X-RAY DIFFRACTIONr_mcangle_it2.32853090
X-RAY DIFFRACTIONr_scbond_it4.03971573
X-RAY DIFFRACTIONr_scangle_it5.403101287
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 79 -
Rwork0.279 1301 -
obs--91.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8611-1.1226-1.37541.97821.25062.96-0.0077-0.1214-0.1261-0.11270.00010.0763-0.00030.10810.0076-0.09590.02620.0008-0.12260.0506-0.133223.16421.428556.8613
23.4326-1.89472.11116.99-3.18113.40180.15530.38590.5401-0.2613-0.4543-0.81240.44320.42790.2989-0.0350.1006-0.0598-0.1580.08490.023616.604935.524824.3965
32.2053-0.48980.06562.778-0.42215.12480.18410.0387-0.291-0.60360.24250.72170.535-0.5593-0.42670.0355-0.0774-0.2394-0.09190.12060.00572.422425.227838.9975
42.5908-0.415-4.72790.11380.48713.8189-0.4673-0.3006-0.16190.64470.09830.1481.31350.29480.3691-0.12810.0139-0.0008-0.03070.0321-0.048126.755719.364262.3112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION2A181 - 275
3X-RAY DIFFRACTION3B1 - 99
4X-RAY DIFFRACTION4P1 - 9

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