- PDB-3ubx: Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex -
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Basic information
Entry
Database: PDB / ID: 3ubx
Title
Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex
Components
Antigen-presenting glycoprotein CD1d1
Beta-2-microglobulin
L363 heavy chain (IGHV9-4*02)
L363 light chain (IGKV13-84*01)
Keywords
IMMUNE SYSTEM / Immunology / mouse CD1d/NKT / mAb
Function / homology
Function and homology information
regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / 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 / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / 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 / positive regulation of type II interferon production / sensory perception of smell / late endosome / 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 / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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
Resolution: 3.1→37.89 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 33.282 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 1.534 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23048
2897
5.1 %
RANDOM
Rwork
0.20199
-
-
-
obs
0.20346
53899
99.9 %
-
all
-
56814
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 66.097 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.02 Å2
-0.01 Å2
0 Å2
2-
-
-0.02 Å2
0 Å2
3-
-
-
0.02 Å2
Refinement step
Cycle: LAST / Resolution: 3.1→37.89 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
12696
0
192
0
12888
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
13304
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.057
1.942
18114
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.505
5
1612
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.933
24.049
568
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.38
15
2076
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.668
15
54
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
1971
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
10072
X-RAY DIFFRACTION
r_gen_planes_other
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
0.095
1.5
8078
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.196
2
13074
X-RAY DIFFRACTION
r_scbond_it
0.356
3
5448
X-RAY DIFFRACTION
r_scangle_it
0.664
4.5
5364
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
2213
TIGHTPOSITIONAL
0.02
0.05
1
A
2213
TIGHTTHERMAL
0.01
0.5
2
B
782
TIGHTPOSITIONAL
0.01
0.05
2
B
782
TIGHTTHERMAL
0.01
0.5
3
L
1654
TIGHTPOSITIONAL
0.01
0.05
3
L
1654
TIGHTTHERMAL
0.01
0.5
4
H
1657
TIGHTPOSITIONAL
0.01
0.05
4
H
1657
TIGHTTHERMAL
0.01
0.5
5
A
54
TIGHTPOSITIONAL
0.01
0.05
5
A
54
TIGHTTHERMAL
0.02
0.5
LS refinement shell
Resolution: 3.1→3.18 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.352
208
-
Rwork
0.318
3818
-
obs
-
-
100 %
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
4.226
1.2759
-1.4275
1.9824
-0.0517
2.3445
-0.0193
0.1875
0.2004
-0.3019
-0.0648
0.1712
-0.0312
-0.2028
0.0841
0.3413
0.1665
0.0329
0.2304
-0.0293
0.2471
-58.7898
-83.4092
38.1217
2
5.0724
-3.2077
-2.5707
4.0592
3.9287
8.2573
-0.1558
0.328
0.0291
-0.1424
-0.1517
0.5085
-0.109
-0.4585
0.3075
0.189
0.0484
-0.0803
0.1083
-0.0437
0.4143
-92.3617
-80.4484
57.0597
3
3.6691
-0.9188
-0.8697
1.2621
1.6764
4.9272
0.3558
0.3521
-0.3015
0.0093
-0.1858
0.103
-0.1063
-0.1871
-0.17
0.1871
0.1295
0.0323
0.1303
0.0134
0.1734
-33.7866
-89.2702
20.445
4
7.7082
-2.5119
0.5941
3.4106
-0.0179
2.7745
0.2497
-0.0347
-0.3362
-0.1188
-0.1152
-0.4458
-0.0517
0.4307
-0.1346
0.2046
0.1012
0.072
0.396
0.0556
0.2784
-0.991
-99.6768
7.5596
5
7.4695
2.1432
-0.1798
1.7997
0.5081
2.3242
0.2401
-0.484
0.8853
0.1798
-0.068
-0.068
-0.6175
0.2679
-0.1722
0.4111
0.0338
0.101
0.193
-0.0561
0.3063
-22.0345
-75.7562
34.1283
6
5.7874
0.591
1.219
3.7159
2.108
8.4667
-0.0467
0.3258
0.5344
-0.6861
0.1118
-0.5253
-0.7894
0.7295
-0.0651
0.38
-0.0371
0.1789
0.4552
0.1757
0.5508
1.708
-84.2549
5.2852
7
6.3319
2.1449
-3.0201
2.2748
-1.9832
5.8956
0.2211
-0.3133
0.2322
0.0194
-0.1591
0.0751
0.238
0.9215
-0.062
0.2287
0.1611
0.0391
0.2651
-0.0976
0.2954
-72.6694
-88.11
62.5438
8
2.633
-1.1858
-1.0087
4.1031
1.0599
2.1507
-0.2182
-0.5288
-0.1305
0.3785
-0.0156
-0.2062
0.074
0.0345
0.2337
0.1938
-0.0023
0.151
0.6042
0.0022
0.2943
-1.7405
-102.1055
-38.2732
9
7.7084
0.04
-4.463
1.5891
-0.8859
7.4224
-0.2281
-0.061
-0.2917
0.1977
0.0325
-0.1106
0.1163
0.1258
0.1956
0.0969
-0.0504
0.0815
0.2225
0.0181
0.3795
26.881
-119.5749
-57.5024
10
3.6714
-2.0336
-0.828
4.9533
2.6523
6.5226
0.0891
-0.0015
-0.2111
-0.1981
-0.1632
0.2022
-0.3233
-0.8406
0.0742
0.1004
-0.0477
0.1462
0.3809
-0.0311
0.3914
6.5421
-114.2208
-63.007
11
2.984
-0.362
-1.4718
0.8028
-0.7626
5.6919
-0.1067
-0.2485
-0.2803
-0.0684
0.1634
0.0061
0.0423
0.2265
-0.0568
0.1222
0.1185
0.0266
0.4036
-0.0851
0.2211
-25.3632
-92.2124
-20.5188
12
6.543
-0.8337
0.8508
3.0258
-0.3888
2.0115
0.1929
-0.0526
0.1194
-0.1683
-0.1024
0.6056
-0.0903
-0.1772
-0.0905
0.1962
0.1184
0.0254
0.4538
-0.0637
0.2419
-58.1265
-81.51
-7.5993
13
3.4726
-3.4617
0.2695
5.8176
-0.1773
2.4577
0.0304
0.1998
0.5577
-0.3208
0.0382
-0.4286
-0.5563
0.4557
-0.0686
0.3324
-0.0504
0.1012
0.438
-0.0673
0.2519
-27.0207
-74.3405
-34.1655
14
4.1971
-0.3694
0.1283
4.7221
-1.4464
6.5589
0.3656
-0.3554
0.7495
0.3735
-0.1149
0.3309
-1.0322
0.1776
-0.2507
0.4006
0.0772
0.0764
0.4061
-0.2373
0.5104
-51.1977
-67.3728
-5.4532
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
6 - 185
2
X-RAY DIFFRACTION
1
A
506 - 512
3
X-RAY DIFFRACTION
1
A
287
4
X-RAY DIFFRACTION
2
A
186 - 286
5
X-RAY DIFFRACTION
3
L
1 - 108
6
X-RAY DIFFRACTION
4
L
109 - 214
7
X-RAY DIFFRACTION
5
H
1 - 120
8
X-RAY DIFFRACTION
6
H
121 - 222
9
X-RAY DIFFRACTION
7
B
1 - 99
10
X-RAY DIFFRACTION
8
D
6 - 185
11
X-RAY DIFFRACTION
8
D
506 - 512
12
X-RAY DIFFRACTION
8
D
287
13
X-RAY DIFFRACTION
9
D
186 - 286
14
X-RAY DIFFRACTION
10
E
2 - 99
15
X-RAY DIFFRACTION
11
I
1 - 108
16
X-RAY DIFFRACTION
12
I
109 - 214
17
X-RAY DIFFRACTION
13
G
1 - 120
18
X-RAY DIFFRACTION
14
G
121 - 222
+
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