- PDB-3b0f: Crystal structure of the UBA domain of p62 and its interaction wi... -
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Basic information
Entry
Database: PDB / ID: 3b0f
Title
Crystal structure of the UBA domain of p62 and its interaction with ubiquitin
Components
Sequestosome-1
Keywords
PROTEIN BINDING / Ubiquitin / Autophagy
Function / homology
Function and homology information
Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / regulation of protein complex stability / endosome organization / non-membrane-bounded organelle assembly / ubiquitin-modified protein reader activity / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / negative regulation of ferroptosis / autolysosome / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / K63-linked polyubiquitin modification-dependent protein binding / mitophagy / autophagosome / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / transcription coregulator activity / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / ionotropic glutamate receptor binding / sarcomere / positive regulation of protein localization to plasma membrane / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / P-body / protein catabolic process / PML body / autophagy / protein import into nucleus / late endosome / signaling receptor activity / protein-macromolecule adaptor activity / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / ubiquitin protein ligase binding / protein-containing complex binding / apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / cytosol Similarity search - Function
Resolution: 1.4→1.45 Å / Redundancy: 11 % / Rmerge(I) obs: 0.356 / % possible all: 82.5
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Processing
Software
Name
Version
Classification
SERGUI
datacollection
SOLVE
phasing
REFMAC
5.5.0072
refinement
HKL-2000
datascaling
Refinement
Method to determine structure: MAD / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.283 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20054
888
5.1 %
RANDOM
Rwork
0.17011
-
-
-
all
0.17167
17323
-
-
obs
0.17167
16435
96.93 %
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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: 11.036 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.8 Å2
0 Å2
0 Å2
2-
-
-0.8 Å2
0 Å2
3-
-
-
1.59 Å2
Refinement step
Cycle: LAST / Resolution: 1.4→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
678
0
5
77
760
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.021
873
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.697
1.978
1207
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.326
5
125
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.195
25.111
45
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.544
15
166
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.295
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.116
0.2
129
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
697
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
1.418
1.5
529
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.024
2
872
X-RAY DIFFRACTION
r_scbond_it
3.027
3
344
X-RAY DIFFRACTION
r_scangle_it
4.179
4.5
327
X-RAY DIFFRACTION
r_rigid_bond_restr
1.7
3
873
X-RAY DIFFRACTION
r_sphericity_free
6.591
3
77
X-RAY DIFFRACTION
r_sphericity_bonded
3.052
3
843
LS refinement shell
Resolution: 1.4→1.436 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.31
69
-
Rwork
0.225
994
-
obs
-
-
82.28 %
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
3.0916
0.433
-1.1005
9.5892
2.0545
3.0336
0.072
-0.1036
0.1072
0.1439
-0.0954
0.0055
-0.1646
0.1376
0.0234
0.0478
-0.0091
0.0187
0.0612
0.0072
0.0758
9.5626
-9.8215
-2.1438
2
6.6639
1.7954
-1.4928
5.2076
1.2763
3.1244
-0.0208
0.1465
0.023
-0.0687
0.0489
0.1869
0.0508
-0.058
-0.028
0.0372
0.0102
0.0025
0.0577
0.0159
0.0586
8.3705
-19.2525
-6.9589
3
4.2482
-5.6342
0.9367
10.3815
-0.4955
2.357
0.174
0.2319
-0.2868
-0.3664
-0.0007
0.267
-0.0379
0.0302
-0.1733
0.0504
-0.018
-0.0007
0.1057
0.0027
0.1174
0.4333
-16.6996
-10.9963
4
3.2031
-0.0237
0.4076
0.9147
0.3597
3.6067
-0.0362
-0.0843
-0.0371
-0.008
0.101
0.0511
0.0466
0.1015
-0.0648
0.0386
0.0041
0.0169
0.0587
0.0024
0.0825
-0.9434
-12.6891
-1.9173
5
4.0391
-0.5687
0.0555
9.8003
-0.6154
1.6031
-0.0142
-0.2599
-0.0925
0.1698
0.113
-0.2324
-0.0614
-0.0503
-0.0988
0.0145
0.0172
-0.0006
0.0826
0.0247
0.0647
4.1736
-16.7869
3.0215
6
10.5177
0.8559
5.6453
5.7217
0.2027
8.6464
0.1028
-0.2046
-0.793
-0.1395
-0.0722
-0.3868
0.4351
0.1649
-0.0306
0.0399
0.0079
0.0115
0.0339
0.0506
0.1581
-1.5268
-24.8038
0.0779
7
7.7033
0.4011
2.0814
1.655
-3.297
7.6598
-0.0385
-0.0548
0.2665
0.1891
0.2246
0.1355
-0.4132
-0.5037
-0.1861
0.1298
0.0385
0.0033
0.1295
-0.0014
0.0218
-21.716
-17.2429
-8.5714
8
5.4191
-3.3838
0.7358
6.7334
-1.3952
3.1592
0.0055
-0.0382
-0.0301
-0.1083
0.1292
-0.0372
-0.0019
0.0251
-0.1347
0.0525
-0.0092
0.0142
0.0406
-0.0208
0.039
-16.0787
-22.3364
-3.1311
9
2.2918
2.0215
-1.5921
6.8541
1.0923
2.3371
0.0081
-0.2472
0.0961
0.0604
0.0752
-0.0051
0.0488
0.29
-0.0833
0.0284
0.0154
-0.0239
0.157
-0.0604
0.0907
-9.2174
-17.6592
-0.7467
10
5.0442
1.9303
2.9708
2.3459
3.8771
6.4823
-0.2951
0.1101
0.6445
-0.1171
0.0857
0.0943
-0.1611
0.0831
0.2094
0.0682
-0.0206
-0.0198
0.0583
-0.0144
0.1906
-10.6423
-14.8478
-11.1535
11
10.1004
0.4805
1.2142
5.1657
1.2073
0.4354
-0.1808
0.2492
-0.2626
-0.2718
0.1543
0.0621
-0.0943
0.062
0.0265
0.0616
-0.0155
0.0113
0.0652
-0.0236
0.0849
-11.0229
-23.4824
-11.7292
12
9.7024
1.805
2.5238
7.6851
1.5372
8.393
-0.108
-0.1124
-0.7286
0.2344
0.0217
-0.1935
0.2411
0.0967
0.0862
0.0262
0.0105
0.0297
0.0475
-0.0201
0.1272
-3.6847
-25.7337
-8.449
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
8 - 15
2
X-RAY DIFFRACTION
2
A
16 - 21
3
X-RAY DIFFRACTION
3
A
22 - 27
4
X-RAY DIFFRACTION
4
A
28 - 37
5
X-RAY DIFFRACTION
5
A
38 - 45
6
X-RAY DIFFRACTION
6
A
46 - 50
7
X-RAY DIFFRACTION
7
B
8 - 13
8
X-RAY DIFFRACTION
8
B
14 - 20
9
X-RAY DIFFRACTION
9
B
21 - 31
10
X-RAY DIFFRACTION
10
B
32 - 39
11
X-RAY DIFFRACTION
11
B
40 - 45
12
X-RAY DIFFRACTION
12
B
46 - 50
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