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- PDB-5vcl: Structure of the Qdm peptide bound to Qa-1a -

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Basic information

Entry
Database: PDB / ID: 5vcl
TitleStructure of the Qdm peptide bound to Qa-1a
Components
  • Beta-2-microglobulin
  • H2-T23 protein
  • Qdm peptide
KeywordsIMMUNE SYSTEM / antigen-presentation / MHC
Function / homology
Function and homology information


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 / cellular defense response / Neutrophil degranulation / 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 ...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 / cellular defense response / Neutrophil degranulation / 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(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 / 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 / defense response / 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 / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / 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 classes I/II-like antigen recognition protein ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, L-D alpha chain / H2-T23 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsYing, G. / Zajonc, D.M.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure of Qa-1a with bound Qa-1 determinant modifier peptide.
Authors: Ying, G. / Wang, J. / Kumar, V. / Zajonc, D.M.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H2-T23 protein
B: Beta-2-microglobulin
P: Qdm peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,66713
Polymers45,1613
Non-polymers50610
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-92 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.207, 75.876, 105.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H2-T23 protein / MHC Qa-1a / Qa-1


Mass: 32514.148 Da / Num. of mol.: 1 / Fragment: UNP residues 21-297
Source method: isolated from a genetically manipulated source
Details: ectodomain residues 21-297 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-T23 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q31153
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Qdm peptide / H-2 class I histocompatibility antigen / L-D alpha chain


Mass: 986.252 Da / Num. of mol.: 1 / Fragment: UNP residues 3-11 / Source method: obtained synthetically / Details: peptide from MHC-class Ia leader sequence / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P01897

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Non-polymers , 3 types, 130 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5% polyethylene glycol 1000, 40% ethylene glycol, 100 mM HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.04→41.42 Å / Num. obs: 34634 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.049 / Rrim(I) all: 0.112 / Χ2: 1.251 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.114.50.5960.8240.2980.671.06793.3
2.11-2.24.70.4490.9050.220.5021.06396.8
2.2-2.34.90.4070.930.2010.4561.14798.9
2.3-2.4250.3430.9380.1690.3831.12199.8
2.42-2.575.10.2690.9540.1320.31.148100
2.57-2.775.10.1990.9690.0980.2221.198100
2.77-3.055.10.1310.9890.0640.1461.227100
3.05-3.4950.0770.9960.0380.0861.31699.9
3.49-4.3950.0610.9970.0290.0681.99399.7
4.39-41.424.80.0370.9980.0180.0421.16599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VJ6

3vj6


Resolution: 2.05→41.42 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.753 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24581 1073 3.2 %RANDOM
Rwork0.21717 ---
obs0.21808 32899 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.05→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 30 120 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193278
X-RAY DIFFRACTIONr_bond_other_d0.0020.022877
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9414447
X-RAY DIFFRACTIONr_angle_other_deg0.90436700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.415382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79423.533167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08615535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4961524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8733.6771537
X-RAY DIFFRACTIONr_mcbond_other1.8733.6771536
X-RAY DIFFRACTIONr_mcangle_it3.0565.51916
X-RAY DIFFRACTIONr_mcangle_other3.0555.4991917
X-RAY DIFFRACTIONr_scbond_it2.0753.9151741
X-RAY DIFFRACTIONr_scbond_other2.0753.9151741
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4135.7772532
X-RAY DIFFRACTIONr_long_range_B_refined5.31840.9073541
X-RAY DIFFRACTIONr_long_range_B_other5.31740.923542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 72 -
Rwork0.365 2152 -
obs--88.96 %

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