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- PDB-3rol: Murine class I major histocompatibility complex H-2Kb in complex ... -

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Basic information

Entry
Database: PDB / ID: 3rol
TitleMurine class I major histocompatibility complex H-2Kb in complex with post-translationally modified LCMV-derived gp34-41 peptide, comprising a nitrotyrosine at position 3
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsIMMUNE SYSTEM / T-cell receptor / MHC / gp34 / NY-gp34 / epitope / post-translational modification / LCMV / MHC CLASS I / IMMUNE ESCAPE / T cell recognition / autoimmunity / T cell receptor / Nitro-tyrosine / Cell surface
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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 / peptide binding / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / 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 / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / defense response to bacterium / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / cytosol
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 / : ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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
PHOSPHATE ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMadhurantakam, C. / Duru, A.D. / Leong, C. / Sandalova, T. / Webb, J.R. / Achour, A.
CitationJournal: PLoS ONE / Year: 2012
Title: Nitro-tyrosination of the immunodominant LCMV epitope gp34-41 alters both its capacity to stabilize H-2Kb and the molecular surface of the MHC complex, affecting TCR recognition
Authors: Madhurantakam, C. / Duru, A.D. / Leong, C. / Sandalova, T. / Webb, J.R. / Achour, A.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
E: Pre-glycoprotein polyprotein GP complex
F: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,28610
Polymers88,8866
Non-polymers4004
Water4,450247
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
E: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5384
Polymers44,4433
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-29 kcal/mol
Surface area18590 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
F: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7486
Polymers44,4433
Non-polymers3053
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-45 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.466, 88.496, 119.050
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 275
2111C1 - 275
1121B1 - 99
2121D1 - 99

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 31777.438 Da / Num. of mol.: 2 / Fragment: unp residues 22-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H-2Kb, H2-K, H2-K1 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: unp residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Pre-glycoprotein polyprotein GP complex


Mass: 961.049 Da / Num. of mol.: 2 / Fragment: unp residues 34-41 / Source method: obtained synthetically / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: Q9QDK7, UniProt: P07399*PLUS

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Non-polymers , 4 types, 251 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / pH: 6.7
Details: 1.8 M NaH2PO4/K2HPO4, 1.5% MPD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.91841
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2008
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→50.3 Å / Num. obs: 32268 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.39 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S7Q

1s7q


Resolution: 2.6→50.3 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.816 / SU B: 12.556 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1654 5.1 %RANDOM
Rwork0.246 ---
obs0.249 30630 100 %-
all-30630 --
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: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.08 Å2
2---0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 24 247 6447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216375
X-RAY DIFFRACTIONr_bond_other_d0.0020.024356
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9488661
X-RAY DIFFRACTIONr_angle_other_deg0.826310525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7785749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21523.489321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.588151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2511548
X-RAY DIFFRACTIONr_chiral_restr0.0730.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217075
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021347
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_it0.5731.53773
X-RAY DIFFRACTIONr_mcbond_other0.1011.51514
X-RAY DIFFRACTIONr_mcangle_it1.10226090
X-RAY DIFFRACTIONr_scbond_it1.532602
X-RAY DIFFRACTIONr_scangle_it2.64.52571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3735tight positional0.030.05
2B1407tight positional0.030.05
1A3735tight thermal0.10.5
2B1407tight thermal0.120.5
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 119 -
Rwork0.236 2283 -
obs--100 %

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