- PDB-7r1o: p62-ZZ domain of the human sequestosome in complex with dusquetide -
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Basic information
Entry
Database: PDB / ID: 7r1o
Title
p62-ZZ domain of the human sequestosome in complex with dusquetide
Components
Dusquetide
Sequestosome-1
Keywords
SIGNALING PROTEIN / dusquetide / p62 / ZZ domain / IDR / innate immune response / signalling protein
Function / homology
Function and homology information
brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / endosomal transport / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / late endosome / protein-macromolecule adaptor activity / Neddylation / signaling receptor activity / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function
Sequestosome-1 / EBI3-associated protein of 60 kDa / EBIAP / p60 / Phosphotyrosine-independent ligand for the Lck ...EBI3-associated protein of 60 kDa / EBIAP / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62
Mass: 5731.634 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13501
#2: Protein/peptide
Dusquetide
Mass: 555.690 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
N
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14.4% PEG 8000, 0.08 M Na-cacodylate pH 6.5, 0.16 M Ca acetate. 200 nl 18 mg/ml p62-ZZ-dusquetide complex + 100 nl seed solution + 300 nl reservoir solution.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0403 Å
Detector
Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 7, 2010 / Details: focusing mirrors
Radiation
Monochromator: bent single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0403 Å / Relative weight: 1
Reflection
Resolution: 2.2→30 Å / Num. obs: 10270 / % possible obs: 98.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.9
Reflection shell
Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1487 / % possible all: 99.2
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
SCALA
3.3.16
datascaling
XSCALE
datascaling
SHELXDE
2006/3
phasing
BUCCANEER
1.4.0
phasing
Coot
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 2.202→24.628 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.577 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.228 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.243
491
4.784 %
Rwork
0.1782
9773
-
all
0.181
-
-
obs
-
10264
98.892 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 33.717 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.9 Å2
0 Å2
1.283 Å2
2-
-
-4.494 Å2
-0 Å2
3-
-
-
0.913 Å2
Refinement step
Cycle: LAST / Resolution: 2.202→24.628 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1594
0
8
102
1704
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.013
1644
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.014
1514
X-RAY DIFFRACTION
r_angle_refined_deg
1.858
1.658
2234
X-RAY DIFFRACTION
r_angle_other_deg
1.294
1.589
3528
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.604
5
212
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.855
20.845
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.724
15
249
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
7.608
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
207
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
1861
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
343
X-RAY DIFFRACTION
r_nbd_refined
0.188
0.2
320
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.19
0.2
1334
X-RAY DIFFRACTION
r_nbtor_refined
0.157
0.2
752
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.081
0.2
744
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.181
0.2
85
X-RAY DIFFRACTION
r_metal_ion_refined
0.099
0.2
6
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.117
0.2
13
X-RAY DIFFRACTION
r_nbd_other
0.128
0.2
36
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.199
0.2
13
X-RAY DIFFRACTION
r_mcbond_it
1.548
2.057
853
X-RAY DIFFRACTION
r_mcbond_other
1.545
2.055
852
X-RAY DIFFRACTION
r_mcangle_it
2.653
3.06
1057
X-RAY DIFFRACTION
r_mcangle_other
2.653
3.063
1058
X-RAY DIFFRACTION
r_scbond_it
1.285
2.128
791
X-RAY DIFFRACTION
r_scbond_other
1.284
2.131
792
X-RAY DIFFRACTION
r_scangle_it
2.142
3.168
1175
X-RAY DIFFRACTION
r_scangle_other
2.141
3.171
1176
X-RAY DIFFRACTION
r_lrange_it
5.157
24.312
1721
X-RAY DIFFRACTION
r_lrange_other
5.125
24.215
1713
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
2.202-2.259
0.253
42
0.225
715
0.227
772
0.884
0.897
98.057
0.191
2.259-2.32
0.254
26
0.189
690
0.192
716
0.851
0.922
100
0.157
2.32-2.387
0.229
36
0.196
661
0.198
700
0.93
0.914
99.5714
0.16
2.387-2.46
0.244
29
0.185
661
0.187
691
0.887
0.925
99.8553
0.162
2.46-2.539
0.266
26
0.181
659
0.183
689
0.889
0.93
99.4194
0.152
2.539-2.628
0.275
28
0.189
597
0.193
628
0.88
0.924
99.5223
0.164
2.628-2.726
0.271
32
0.188
588
0.192
622
0.874
0.929
99.6785
0.162
2.726-2.835
0.267
28
0.184
592
0.188
622
0.905
0.928
99.6785
0.16
2.835-2.96
0.251
18
0.183
541
0.186
559
0.931
0.937
100
0.165
2.96-3.102
0.186
33
0.155
538
0.157
574
0.949
0.953
99.4773
0.143
3.102-3.267
0.243
30
0.174
507
0.178
539
0.932
0.95
99.6289
0.16
3.267-3.461
0.226
27
0.165
468
0.168
497
0.941
0.959
99.5976
0.159
3.461-3.695
0.208
19
0.185
462
0.186
483
0.943
0.951
99.5859
0.178
3.695-3.984
0.181
19
0.163
419
0.164
444
0.94
0.955
98.6487
0.162
3.984-4.352
0.242
19
0.165
393
0.169
417
0.939
0.958
98.801
0.165
4.352-4.847
0.205
13
0.13
363
0.132
383
0.95
0.972
98.1723
0.132
4.847-5.561
0.269
23
0.179
304
0.185
333
0.936
0.958
98.1982
0.188
5.561-6.726
0.238
21
0.202
269
0.205
299
0.955
0.941
96.99
0.213
6.726-9.176
0.372
15
0.206
214
0.212
237
0.8
0.944
96.6245
0.216
9.176-24.628
0.382
7
0.217
132
0.224
162
0.906
0.955
85.8025
0.237
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
0.5541
0.0583
-0.5743
3.1721
-0.0977
0.6062
-0.0467
-0.0183
-0.0204
-0.016
0.0367
-0.0479
0.0241
-0.0125
0.01
0.0916
0.0133
0.0475
0.1938
0.0003
0.0283
28.3006
-10.3096
10.0504
2
1.1605
0.0296
0.4033
5.5708
-0.5827
0.7608
-0.1094
0.4389
-0.1454
0.8962
0.0528
-0.7203
-0.2615
-0.1365
0.0566
0.1848
0.0278
-0.1076
0.312
-0.0736
0.1117
35.9218
-0.5104
21.1671
3
2.0014
2.8804
0.1357
6.3168
-0.226
0.1142
-0.1877
0.0548
0.5512
-0.5485
0.2141
1.1948
0.0562
0.0438
-0.0264
0.0656
0.019
-0.0841
0.1997
0.0753
0.2721
-0.8194
13.0221
12.4758
4
0.2477
-0.3518
-0.4181
2.3956
-0.0491
0.9745
-0.0101
-0.0182
-0.0244
0.0401
0.0012
0.2313
0.0556
0.1243
0.009
0.1403
-0.0031
0.1027
0.1809
0.0026
0.0937
9.2769
3.3973
21.3794
5
11.6782
2.929
-1.3976
1.1418
0.3121
1.2462
-0.2631
-0.3348
0.1069
0.0912
0.1293
0.1091
0.2874
0.3726
0.1338
0.1405
0.0555
0.0233
0.1479
0.0129
0.057
18.9198
-1.1118
27.9685
6
3.7007
2.2405
4.0861
10.716
-0.0974
5.2197
-0.2237
-0.3936
-0.0731
-0.4831
0.5251
0.7301
-0.1369
-0.6345
-0.3014
0.1093
-0.0266
-0.0034
0.2076
0.0715
0.0713
20.8908
-13.8134
2.3977
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
ALL
AAA
120 - 172
2
X-RAY DIFFRACTION
2
ALL
BBB
124 - 171
3
X-RAY DIFFRACTION
3
ALL
CCC
121 - 171
4
X-RAY DIFFRACTION
4
ALL
DDD
120 - 172
5
X-RAY DIFFRACTION
5
ALL
EEE
1 - 5
6
X-RAY DIFFRACTION
6
ALL
FFF
1 - 4
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