- PDB-3p77: Crystal Structures of the Chicken YF1*7.1 molecule -
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Basic information
Entry
Database: PDB / ID: 3p77
Title
Crystal Structures of the Chicken YF1*7.1 molecule
Components
Beta-2-microglobulin
MHC Rfp-Y class I alpha chain
Keywords
IMMUNE SYSTEM / IG-LIKE C1-TYPE (IMMUNOGLOBULIN-LIKE) DOMAIN / HISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information
ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / 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 / 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 / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / membrane / cytosol Similarity search - Function
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 ...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
ACETATE ION / TRIETHYLENE GLYCOL / Beta-2-microglobulin / MHC Rfp-Y class I alpha chain Similarity search - Component
Resolution: 1.6→19.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.348 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21552
2193
5.1 %
RANDOM
Rwork
0.17391
-
-
-
all
0.17601
40891
-
-
obs
0.17601
40891
89.82 %
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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: MASK
Displacement parameters
Biso mean: 13.861 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0.03 Å2
2-
-
0.06 Å2
0 Å2
3-
-
-
-0.05 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→19.65 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2988
0
50
382
3420
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
3213
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2234
X-RAY DIFFRACTION
r_angle_refined_deg
1.403
1.944
4362
X-RAY DIFFRACTION
r_angle_other_deg
0.835
3
5415
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.171
5
395
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.642
23.642
162
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.136
15
518
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.464
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
437
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
3602
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
689
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
0.68
1.5
1898
X-RAY DIFFRACTION
r_mcbond_other
0.2
1.5
761
X-RAY DIFFRACTION
r_mcangle_it
1.224
2
3069
X-RAY DIFFRACTION
r_scbond_it
2.065
3
1315
X-RAY DIFFRACTION
r_scangle_it
3.26
4.5
1279
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.6→1.641 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.233
154
-
Rwork
0.206
3127
-
obs
-
-
93.21 %
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
1.1359
0.0977
-0.0498
0.8114
0.4949
1.7466
0.0032
0.0176
-0.0471
-0.0528
-0.0071
-0.0353
-0.0626
-0.0206
0.0039
0.0417
-0.0068
0.001
0.0049
0.0116
0.0556
25.5523
9.7156
4.3404
2
2.6363
1.3299
0.3242
3.349
0.2184
1.8827
-0.0164
-0.0798
-0.2379
0.1635
-0.0616
0.0535
0.2743
-0.1387
0.078
0.0811
-0.009
0.0243
0.0945
0.0223
0.0486
10.5167
-17.5148
23.3454
3
2.1575
0.1709
-1.2416
1.3556
-0.6734
3.714
-0.0674
0.0142
-0.1039
-0.014
0.0862
0.1082
0.041
-0.2445
-0.0188
0.0261
0.0041
-0.0006
0.0481
0.007
0.0642
2.4974
-0.0846
13.9016
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
0 - 179
2
X-RAY DIFFRACTION
2
A
180 - 273
3
X-RAY DIFFRACTION
3
B
1 - 99
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