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- PDB-1s7v: Crystal structures of the murine class I major histocompatibility... -

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Basic information

Entry
Database: PDB / ID: 1s7v
TitleCrystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 index peptide and three of its escape variants
Components
  • Beta-2-microglobulin
  • Glycoprotein 9-residue peptide
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / LCMV / MHC class I / immune escape
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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / host cell Golgi membrane / 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 / 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 / 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 / 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 / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / immune response / lysosomal membrane / external side of plasma 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 / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / 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 / Beta-2-Microglobulin ...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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVelloso, L.M. / Michaelsson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
CitationJournal: J.Immunol. / Year: 2004
Title: Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition.
Authors: Velloso, L.M. / Michaelsson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE THE CYSTEINE IN THE ORIGINAL SEQUENCE IS REPLACED INTENTIONALLY BY A METHIONINE TO AVOID ...SEQUENCE THE CYSTEINE IN THE ORIGINAL SEQUENCE IS REPLACED INTENTIONALLY BY A METHIONINE TO AVOID OXIDATION OF THE PEPTIDE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)102,3296
Polymers102,3296
Non-polymers00
Water7,999444
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,1653
Polymers51,1653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-18 kcal/mol
Surface area18360 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,1653
Polymers51,1653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-18 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.469, 91.184, 92.147
Angle α, β, γ (deg.)90.00, 125.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
71A
81D
91A
101D
111A
121D
131A
141D
151A
161D
171A
181D
191A
201D
211A
221D
12B
22E
32B
42E
52B
62E
72B
82E
92B
102E
112B
122E
132B
142E
152B
162E
172B
182E
192B
202E
212B
222E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO1AA1 - 21 - 2
211GLYGLYPROPRO1DD1 - 21 - 2
321SERSERSERSER1AA4 - 924 - 92
421SERSERSERSER1DD4 - 924 - 92
531THRTHRLEULEU1AA94 - 16894 - 168
631THRTHRLEULEU1DD94 - 16894 - 168
741ARGARGALAALA1AA170 - 187170 - 187
841ARGARGALAALA1DD170 - 187170 - 187
951PROPROTYRTYR1AA193 - 262193 - 262
1051PROPROTYRTYR1DD193 - 262193 - 262
1161GLUGLUPROPRO1AA264 - 276264 - 276
1261GLUGLUPROPRO1DD264 - 276264 - 276
1371HISHISHISHIS3AA33
1471HISHISHISHIS3DD33
1581HISHISHISHIS3AA9393
1681HISHISHISHIS3DD9393
1791HISHISHISHIS3AA169169
1891HISHISHISHIS3DD169169
19101HISHISHISHIS3AA188 - 192188 - 192
20101HISHISHISHIS3DD188 - 192188 - 192
21111HISHISHISHIS3AA263263
22111HISHISHISHIS3DD263263
112ILEILEARGARG1BB1 - 121 - 12
212ILEILEARGARG1EE1 - 121 - 12
322PROPROPHEPHE1BB14 - 3014 - 30
422PROPROPHEPHE1EE14 - 3014 - 30
532PROPROPROPRO1BB32 - 3332 - 33
632PROPROPROPRO1EE32 - 3332 - 33
742ILEILEALAALA1BB35 - 6635 - 66
842ILEILEALAALA1EE35 - 6635 - 66
952THRTHRHISHIS1BB68 - 8468 - 84
1052THRTHRHISHIS1EE68 - 8468 - 84
1162ASPASPMETMET1BB85 - 9985 - 99
1262ASPASPMETMET1EE85 - 9985 - 99
1372HISHISHISHIS3BB1313
1472HISHISHISHIS3EE1313
1582HISHISHISHIS3BB3131
1682HISHISHISHIS3EE3131
1792HISHISHISHIS3BB3434
1892HISHISHISHIS3EE3434
19102HISHISHISHIS3BB6767
20102HISHISHISHIS3EE6767
21112HISHISHISHIS3BB8484
22112HISHISHISHIS3EE8484
113LYSLYSMETMET1CC1 - 91 - 9
213LYSLYSMETMET1FF1 - 91 - 9

NCS ensembles :
ID
1
2
3

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2DB


Mass: 38449.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01887
#3: Protein/peptide Glycoprotein 9-residue peptide


Mass: 1011.215 Da / Num. of mol.: 2 / Mutation: F6L / Source method: obtained synthetically
Details: The peptide was chemically synthesized, the sequence of the peptide is naturally found in Lymphocytic choriomeningitis virus
References: UniProt: P07399
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 3.18 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 26, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. all: 55257 / Num. obs: 52163 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.257 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N5A

1n5a


Resolution: 2.2→32.44 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.091 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.277 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26678 2639 5.1 %RANDOM
Rwork0.2256 ---
obs0.22761 49523 94.41 %-
all-55257 --
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: 19.852 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å21.62 Å2
2--1.72 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6207 0 0 444 6651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216400
X-RAY DIFFRACTIONr_bond_other_d0.0040.025462
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9318688
X-RAY DIFFRACTIONr_angle_other_deg0.924312728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535762
X-RAY DIFFRACTIONr_chiral_restr0.0870.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027186
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021366
X-RAY DIFFRACTIONr_nbd_refined0.2330.21523
X-RAY DIFFRACTIONr_nbd_other0.2620.26823
X-RAY DIFFRACTIONr_nbtor_other0.090.23690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2335
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.216
X-RAY DIFFRACTIONr_mcbond_it0.6341.53819
X-RAY DIFFRACTIONr_mcangle_it1.14526131
X-RAY DIFFRACTIONr_scbond_it1.67132581
X-RAY DIFFRACTIONr_scangle_it2.6614.52557
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4064tight positional0.070.05
2B1511tight positional0.040.05
3C136tight positional0.030.05
1A87loose positional0.365
2B50loose positional0.15
1A4064tight thermal0.240.5
2B1511tight thermal0.230.5
3C136tight thermal0.210.5
1A87loose thermal1.4110
2B50loose thermal1.3310
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 131
Rwork0.346 2598

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