Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate
Components
Polyubiquitin
Protein kinase OspG
Ubiquitin-conjugating enzyme E2 L3
Keywords
UNKNOWN FUNCTION / PROTEIN BINDING / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / kinase fold / inhibition of NF-kB pathway
Function / homology
Function and homology information
Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Transferases; Transferring phosphorus-containing groups / cell cycle phase transition / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / ubiquitin-protein transferase activator activity / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein K11-linked ubiquitination / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Ub-specific processing proteases / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / Regulation of necroptotic cell death / modification-dependent protein catabolic process / protein polyubiquitination / ubiquitin-protein transferase activity / protein tag activity / host cell / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / kinase activity / ubiquitin-dependent protein catabolic process / cell population proliferation / protein autophosphorylation / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function
Monochromator: dcm WITH CRYO-COOLED 1ST CRYSTAL SAGITALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97949 Å / Relative weight: 1
Reflection
Resolution: 1.87→50 Å / Num. obs: 40758 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 36.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)
Redundancy (%)
Diffraction-ID
% possible all
Rmerge(I) obs
1.87-1.9
11.1
1
100
1.9-1.94
11.1
1
100
1.94-1.97
11.1
1
100
0.95
1.97-2.01
11.2
1
100
0.782
2.01-2.06
11.1
1
100
0.64
2.06-2.11
11.1
1
100
0.501
2.11-2.16
11.2
1
100
0.483
2.16-2.22
11.1
1
100
0.362
2.22-2.28
11.2
1
100
0.276
2.28-2.36
11.1
1
100
0.228
2.36-2.44
11.2
1
100
0.206
2.44-2.54
11.1
1
100
0.175
2.54-2.65
11.1
1
100
0.15
2.65-2.79
11
1
100
0.135
2.79-2.97
11.1
1
100
0.119
2.97-3.2
11
1
100
0.102
3.2-3.52
11
1
100
0.091
3.52-4.03
10.9
1
100
0.084
4.03-5.07
10.8
1
100
0.077
5.07-50
10.1
1
99.4
0.076
-
Phasing
Phasing
Method: molecular replacement
Phasing MR
Rfactor: 54.98
Highest resolution
Lowest resolution
Rotation
2.5 Å
44.76 Å
Translation
2.5 Å
44.76 Å
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
2.1.4
phasing
PHENIX
1.9_1692
refinement
PDB_EXTRACT
3.14
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.869→44.758 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2315
2044
5.02 %
Rwork
0.1846
-
-
obs
0.1869
40691
99.65 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 55.09 Å2
Refinement step
Cycle: LAST / Resolution: 1.869→44.758 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3218
0
0
237
3455
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.014
3326
X-RAY DIFFRACTION
f_angle_d
1.465
4509
X-RAY DIFFRACTION
f_dihedral_angle_d
14.045
1290
X-RAY DIFFRACTION
f_chiral_restr
0.071
498
X-RAY DIFFRACTION
f_plane_restr
0.007
592
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.8686-1.9121
0.3179
115
0.277
2425
X-RAY DIFFRACTION
95
1.9121-1.9599
0.2896
141
0.2456
2548
X-RAY DIFFRACTION
100
1.9599-2.0129
0.2972
159
0.2235
2495
X-RAY DIFFRACTION
100
2.0129-2.0721
0.2341
123
0.2146
2572
X-RAY DIFFRACTION
100
2.0721-2.139
0.2391
147
0.2017
2549
X-RAY DIFFRACTION
100
2.139-2.2155
0.2256
148
0.2015
2558
X-RAY DIFFRACTION
100
2.2155-2.3042
0.2294
128
0.1852
2565
X-RAY DIFFRACTION
100
2.3042-2.409
0.2547
136
0.1964
2577
X-RAY DIFFRACTION
100
2.409-2.536
0.2521
145
0.1949
2542
X-RAY DIFFRACTION
100
2.536-2.6949
0.243
136
0.1941
2599
X-RAY DIFFRACTION
100
2.6949-2.9029
0.2823
134
0.2046
2574
X-RAY DIFFRACTION
100
2.9029-3.195
0.2205
129
0.1945
2609
X-RAY DIFFRACTION
100
3.195-3.6571
0.2236
115
0.177
2630
X-RAY DIFFRACTION
100
3.6571-4.6069
0.1912
141
0.1525
2642
X-RAY DIFFRACTION
100
4.6069-44.7711
0.2368
147
0.1838
2762
X-RAY DIFFRACTION
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
1.8694
0.1351
-0.8735
2.6196
-1.1003
2.317
-0.0601
0.0315
-0.1242
0.0372
0.0582
-0.1128
0.1589
0.0777
-0.0079
0.2279
0.0329
0.0095
0.2266
-0.012
0.2328
26.6417
-54.9165
-2.6054
2
3.5316
0.6206
0.4754
4.0551
-0.3487
6.0964
0.0064
0.4638
0.6557
0.0398
0.1194
-0.1301
-0.603
0.0976
-0.1646
0.3529
-0.009
0.0799
0.3112
0.1037
0.4177
37.019
-34.1873
-16.4966
3
1.4169
-0.6584
0.0062
5.0821
-2.1578
4.2598
0.0028
-0.1023
0.1814
0.277
0.0342
0.2436
-0.74
-0.2517
-0.0232
0.3514
0.0456
-0.0388
0.3452
-0.0591
0.2772
2.5504
-30.7163
-5.6469
4
0.5118
-0.4386
0.1271
0.3805
-0.2623
0.6543
-0.0757
-0.0738
0.0456
0.0802
0.0435
0.004
-0.0334
-0.0857
0.0271
0.3811
0.0006
-0.001
0.3782
0.0078
0.2961
19.1926
-45.446
-3.4114
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
( CHAINAANDRESID26:193 )
A
26 - 193
2
X-RAY DIFFRACTION
2
( CHAINBANDRESID1:76 )
B
1 - 76
3
X-RAY DIFFRACTION
3
( CHAINCANDRESID0:154 )
C
0 - 154
4
X-RAY DIFFRACTION
4
( CHAINAANDRESID201:324 ) OR ( CHAINCANDRESID201:289 ) OR ( CHAINBANDRESID101:124 )
A
201 - 324
5
X-RAY DIFFRACTION
4
( CHAINAANDRESID201:324 ) OR ( CHAINCANDRESID201:289 ) OR ( CHAINBANDRESID101:124 )
C
201 - 289
6
X-RAY DIFFRACTION
4
( CHAINAANDRESID201:324 ) OR ( CHAINCANDRESID201:289 ) OR ( CHAINBANDRESID101:124 )
B
101 - 124
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi