HLA class II histocompatibility antigen, DP alpha 1 chain
HLA-DP2 beta chain linked with DRa peptide
Keywords
IMMUNE SYSTEM / HLA / MHC / Immune / Disulfide bond / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane
Function / homology
Function and homology information
MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of type II interferon production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / cell surface / membrane / plasma membrane Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen, DP alpha 1 chain / HLA class II histocompatibility antigen DP beta chain Similarity search - Component
Resolution: 3.25→3.283 Å / Redundancy: 6 % / % possible all: 89.1
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHASER
phasing
REFMAC
5.3.0040
refinement
HKL-2000
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.907 / SU B: 49.178 / SU ML: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.439 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25094
645
5.1 %
RANDOM
Rwork
0.21693
-
-
-
obs
0.21865
11332
86.16 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 93.721 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.94 Å2
2.97 Å2
0 Å2
2-
-
5.94 Å2
0 Å2
3-
-
-
-8.91 Å2
Refinement step
Cycle: LAST / Resolution: 3.25→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3114
0
42
0
3156
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
3252
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.49
1.947
4426
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.719
5
375
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.92
24.246
179
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.43
15
506
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.275
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
467
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
2564
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.228
0.2
1383
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.319
0.2
2177
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.182
0.2
89
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
0.221
0.2
26
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.079
0.2
5
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
0.364
1.5
1930
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.672
2
3076
X-RAY DIFFRACTION
r_scbond_it
0.957
3
1488
X-RAY DIFFRACTION
r_scangle_it
1.661
4.5
1350
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3.25→3.283 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.37
58
-
Rwork
0.338
902
-
obs
-
-
88.89 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
1.8359
0.4828
-1.6206
2.3171
-0.2668
4.3693
0.0777
-0.1584
0.2297
-0.0476
-0.0119
0.2631
-0.8404
-0.5076
-0.0659
-0.3006
-0.0666
-0.1266
-0.2296
-0.045
-0.2938
54.04
-37.281
5.379
2
2.5036
0.6654
-1.3225
1.927
-0.8028
4.2617
-0.0501
-0.1263
-0.2653
-0.053
-0.0407
-0.0557
0.1003
-0.3247
0.0908
-0.421
-0.2041
-0.1996
-0.3195
-0.0155
-0.2652
51.859
-53.429
2.219
3
1.6055
-3.7948
0.2394
11.0906
-3.0525
3.0329
0.5502
0.7031
0.7665
-1.4606
-0.9247
-0.6661
1.5095
1.0758
0.3745
-0.2836
-0.1997
0.0796
-0.4628
0.0229
-0.0249
70.264
-41.69
-11.035
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 181
2
X-RAY DIFFRACTION
2
B
3 - 189
3
X-RAY DIFFRACTION
3
B
-22 - -8
+
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