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- PDB-1n59: Crystal structure of the Murine class I Major Histocompatibility ... -

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Basic information

Entry
Database: PDB / ID: 1n59
TitleCrystal structure of the Murine class I Major Histocompatibility Complex of H-2KB, B2-Microglobulin, and A 9-Residue immunodominant peptide epitope gp33 derived from LCMV
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus
KeywordsIMMUNE SYSTEM / Murine MHC / viral escape / LCMV / immunodominant epitope
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 exogenous peptide antigen via MHC class I / 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 / host cell Golgi membrane / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / 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 / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / defense response to bacterium / 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 / 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 / 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, K-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAchour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Karre, K. / Sandalova, T. / Schneider, G.
CitationJournal: Immunity / Year: 2002
Title: A Structural Basis for LCMV Immune Evasion. Subversion of H-2D(b) and H-2K(b) Presentation of gp33 Revealed by Comparative Crystal Structure Analyses.
Authors: Achour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Karre, K. / Sandalova, T. / Schneider, G.
History
DepositionNov 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 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

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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, K-B alpha chain
B: Beta-2-microglobulin
P: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
Q: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus


Theoretical massNumber of molelcules
Total (without water)89,2486
Polymers89,2486
Non-polymers00
Water1,51384
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus


Theoretical massNumber of molelcules
Total (without water)44,6243
Polymers44,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-21 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
Q: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus


Theoretical massNumber of molelcules
Total (without water)44,6243
Polymers44,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-21 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.551, 88.574, 120.090
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13P
23Q

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISARG3AA3 - 2733 - 273
21HISARG3CD3 - 2733 - 273
12ILEASP3BB1 - 981 - 98
22ILEASP3DE1 - 981 - 98
13ALATHR1PC2 - 82 - 8
23ALATHR1QF2 - 82 - 8

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 31874.551 Da / Num. of mol.: 2 / Fragment: Extracellular fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus


Mass: 1045.232 Da / Num. of mol.: 2 / Mutation: C9M / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED / References: UniProt: Q9QDK7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.02 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.85 Msodium potassium phosphate1reservoir
21 %MPD1reservoir
35 mg/mlprotein1drop
420 mMTris-Cl1droppH7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.018 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 2000
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 46919 / Num. obs: 46919 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 43.1 Å2 / Rsym value: 0.13 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.06 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 733 / Rsym value: 0.242 / % possible all: 62.2
Reflection
*PLUS
Highest resolution: 2.95 Å / Num. obs: 20422 / % possible obs: 86.8 % / Num. measured all: 46919 / Rmerge(I) obs: 0.13
Reflection shell
*PLUS
Highest resolution: 2.95 Å / Lowest resolution: 3 Å / % possible obs: 62.2 % / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OSZ

1osz


Resolution: 2.95→19.92 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.849 / SU B: 22.217 / SU ML: 0.426 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.504
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 986 5 %RANDOM
Rwork0.22904 ---
all0.2319 18616 --
obs0.23195 18616 100 %-
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: 26.531 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å24.55 Å2
2---7.69 Å20 Å2
3---9.75 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 0 84 6344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216443
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9348753
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8223760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.087151139
X-RAY DIFFRACTIONr_chiral_restr0.1070.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3070.33183
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.5558
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.345
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4010.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9351.53819
X-RAY DIFFRACTIONr_mcangle_it1.79226175
X-RAY DIFFRACTIONr_scbond_it2.15832624
X-RAY DIFFRACTIONr_scangle_it3.6994.52578
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
1A1090tight positional0.070.05
2B1902tight positional0.080.05
3C1957tight positional0.060.05
1A1116loose positional0.285
2B1116loose positional0.025
3C1116loose positional05
1A1090tight thermal0.150.5
2B1902tight thermal0.710.5
3C1957tight thermal1.50.5
1A1116loose thermal2.5110
2B1116loose thermal3.7510
3C1116loose thermal4.5810
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 51
Rwork0.291 1021
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)
10.4080.5765-0.09131.3518-0.02050.02960.0086-0.15770.04810.1581-0.07290.07780.1184-0.00340.06430.302-0.0050.00760.2840.00360.10318.1593.25313.604
22.97971.88110.86533.54611.21530.56270.0291-0.0220.05460.01030.01910.00380.00580.0289-0.04830.19280.00680.01480.23460.03520.142216.952-9.7330.624
373.809423.65022.239110.14941.33796.9419-0.5116-0.85371.1488-1.0759-0.35860.6349-0.1198-0.44150.87020.15370.1247-0.02330.14850.0220.090924.50419.82110.51
40.1607-0.8759-0.2112.6679-0.87421.39440.0499-0.045-0.0196-0.1021-0.1171-0.08780.07190.03910.06720.7001-0.02240.12570.488-0.00590.21042.3427.3945.987
53.1705-2.28310.20223.90380.17391.8054-0.02280.01170.12720.2373-0.24070.18460.2353-0.12480.26350.7971-0.07280.150.532-0.05450.191-8.4920.41352.982
613.792421.627930.95150.569816.981647.1264-0.20291.4411-2.03840.91821.285-0.6182-1.00120.5927-1.0820.4482-0.08420.04740.5691-0.04230.2233.942-9.26152.923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1822 - 182
2X-RAY DIFFRACTION1AA183 - 273183 - 273
3X-RAY DIFFRACTION2BB1 - 981 - 98
4X-RAY DIFFRACTION3PC2 - 82 - 8
5X-RAY DIFFRACTION4CD2 - 1822 - 182
6X-RAY DIFFRACTION4CD183 - 273183 - 273
7X-RAY DIFFRACTION5DE1 - 981 - 98
8X-RAY DIFFRACTION6QF2 - 82 - 8
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.89

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