- PDB-3rol: Murine class I major histocompatibility complex H-2Kb in complex ... -
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Basic information
Entry
Database: PDB / ID: 3rol
Title
Murine 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
Keywords
IMMUNE 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
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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.295
1654
5.1 %
RANDOM
Rwork
0.246
-
-
-
obs
0.249
30630
100 %
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all
-
30630
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-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 31.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.03 Å2
0 Å2
-0.08 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
-0.03 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→50.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6176
0
24
247
6447
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.021
6375
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
4356
X-RAY DIFFRACTION
r_angle_refined_deg
1.285
1.948
8661
X-RAY DIFFRACTION
r_angle_other_deg
0.826
3
10525
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.778
5
749
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.215
23.489
321
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.588
15
1037
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.251
15
48
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
890
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
7075
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1347
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.573
1.5
3773
X-RAY DIFFRACTION
r_mcbond_other
0.101
1.5
1514
X-RAY DIFFRACTION
r_mcangle_it
1.102
2
6090
X-RAY DIFFRACTION
r_scbond_it
1.5
3
2602
X-RAY DIFFRACTION
r_scangle_it
2.6
4.5
2571
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
3735
tightpositional
0.03
0.05
2
B
1407
tightpositional
0.03
0.05
1
A
3735
tightthermal
0.1
0.5
2
B
1407
tightthermal
0.12
0.5
LS refinement shell
Resolution: 2.6→2.67 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.318
119
-
Rwork
0.236
2283
-
obs
-
-
100 %
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