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- PDB-3vj6: Structure of the MHC class Ib molecule Qa-1b -

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Basic information

Entry
Database: PDB / ID: 3vj6
TitleStructure of the MHC class Ib molecule Qa-1b
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-37 alpha chain
  • Qdm peptide
KeywordsIMMUNE SYSTEM / MHC-classIb / Immunoglobulin fold / Peptide presentation / CD94-NKG2A/C receptors
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / inner ear development / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response ...antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / inner ear development / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, L-D alpha chain / H-2 class I histocompatibility antigen, D-37 alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZeng, L. / Clements, C.S. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2012
Title: A structural basis for antigen presentation by the MHC class Ib molecule, Qa-1b
Authors: Zeng, L. / Sullivan, L.C. / Vivian, J.P. / Walpole, N.G. / Harpur, C.M. / Rossjohn, J. / Clements, C.S. / Brooks, A.G.
History
DepositionOct 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 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: H-2 class I histocompatibility antigen, D-37 alpha chain
B: Beta-2-microglobulin
P: Qdm peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4037
Polymers45,1693
Non-polymers2354
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-43 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.268, 72.833, 95.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class I histocompatibility antigen, D-37 alpha chain


Mass: 32346.816 Da / Num. of mol.: 1 / Fragment: Qa-1b extracellular domain, UNP residues 21-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-T23 / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06339
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide Qdm peptide


Mass: 986.252 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthesised peptide from MHC-classIa leader sequence
Source: (synth.) Mus musculus (house mouse) / References: UniProt: P01897
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 6% PEG 4000, 10mM NiCl2, 0.1M sodium acetate, pH 6.3. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→42 Å / Num. all: 33622 / Num. obs: 33622 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 31.5
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESV

2esv


Resolution: 1.9→41.449 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1701 5.07 %random
Rwork0.2008 ---
obs0.2029 33533 99.69 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.888 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 85.43 Å2 / Biso mean: 31.029 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.1177 Å20 Å2-0 Å2
2--0.2488 Å20 Å2
3----0.1311 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 4 263 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063283
X-RAY DIFFRACTIONf_angle_d1.0834465
X-RAY DIFFRACTIONf_dihedral_angle_d14.9681226
X-RAY DIFFRACTIONf_chiral_restr0.077457
X-RAY DIFFRACTIONf_plane_restr0.005588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8956-1.96340.30661580.2912310098
1.9634-2.0420.33221620.23153158100
2.042-2.13490.27771730.22183133100
2.1349-2.24740.27741760.20633125100
2.2474-2.38820.28021670.20873161100
2.3882-2.57260.26721880.20943144100
2.5726-2.83150.28771640.20743199100
2.8315-3.2410.24961730.19493195100
3.241-4.08280.20481670.17383242100
4.0828-41.45920.19941730.19583375100

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