- PDB-2xew: Crystal structure of K11-linked diubiquitin -
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Basic information
Entry
Database: PDB / ID: 2xew
Title
Crystal structure of K11-linked diubiquitin
Components
UBIQUITIN
Keywords
CELL CYCLE / PROTEIN DEGRADATION / PROTEASOME / DEUBIQUITINATION
Function / homology
Function and homology information
: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta Similarity search - Domain/homology
Resolution: 2.2→24.918 Å / SU ML: 0.32 / σ(F): 0.02 / Phase error: 27.53 / Stereochemistry target values: ML Details: RESIDUES LACKING DISCERNIBLE ELECTRON DENSITY WERE MODELED WITH OCCUPANCY SET TO 0.00. ISOPEPTIDE BONDS BETWEEN LYS11 AND THE C-TERMINAL GLY76 OF NEIGHBORING MOLECULES ARE PRESENT IN THIS ENTRY.
Rfactor
Num. reflection
% reflection
Rfree
0.2515
3319
5 %
Rwork
0.205
-
-
obs
0.2073
65987
91.4 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.491 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
0.0121 Å2
0 Å2
0 Å2
2-
-
0.1218 Å2
-0 Å2
3-
-
-
-0.1339 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→24.918 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7115
0
101
651
7867
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
7414
X-RAY DIFFRACTION
f_angle_d
0.978
9961
X-RAY DIFFRACTION
f_dihedral_angle_d
17.426
2968
X-RAY DIFFRACTION
f_chiral_restr
0.06
1174
X-RAY DIFFRACTION
f_plane_restr
0.004
1294
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2-2.2786
0.3276
292
0.2547
5659
X-RAY DIFFRACTION
84
2.2786-2.3698
0.3262
340
0.2463
5859
X-RAY DIFFRACTION
87
2.3698-2.4775
0.2753
335
0.2248
6045
X-RAY DIFFRACTION
89
2.4775-2.608
0.27
302
0.2031
6173
X-RAY DIFFRACTION
91
2.608-2.7712
0.2628
334
0.2121
6252
X-RAY DIFFRACTION
92
2.7712-2.9848
0.2978
345
0.2246
6357
X-RAY DIFFRACTION
93
2.9848-3.2846
0.2543
334
0.1939
6559
X-RAY DIFFRACTION
96
3.2846-3.7585
0.2243
351
0.1727
6598
X-RAY DIFFRACTION
96
3.7585-4.73
0.1917
357
0.1636
6569
X-RAY DIFFRACTION
95
4.73-24.9195
0.2327
329
0.213
6597
X-RAY DIFFRACTION
91
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
2.5308
-0.5141
0.3601
1.7676
0.3903
0.6123
-0.2823
-0.0979
-0.1859
0.13
0.2797
0.0552
0.1183
0.0342
0.0127
0.0724
0.026
0.0635
0.0745
0.0082
0.1019
88.7325
-12.0543
150.408
2
1.4749
1.5949
-0.4888
2.1488
-1.249
1.4196
0.1536
-0.0379
0.3867
0.0896
-0.0069
0.2758
-0.1882
0.1584
-0.1339
0.0891
-0.0456
0.0637
0.0755
-0.0125
0.1099
64.7489
-7.2215
150.2267
3
2.0434
-1.5621
-1.508
1.5946
0.9731
1.4895
0.1867
0.0176
0.2396
-0.0634
-0.0177
-0.2525
-0.0278
-0.0078
-0.0646
0.1149
0.0881
0.0421
0.0849
-0.0068
0.111
69.569
16.7394
150.41
4
0.9585
0.7456
-0.0865
1.6108
0.8561
0.8266
0.111
-0.0539
0.0313
0.07
-0.0412
-0.0788
-0.0617
0.117
-0.0245
0.1119
-0.0535
0.0421
0.1014
-0.0136
0.107
93.7125
11.8621
150.3931
5
3.6709
0.3899
-2.5985
2.8894
-1.0675
2.8295
0.1349
1.1185
0.5401
-0.4234
0.1022
-0.0633
-0.3654
-1.0442
-0.3181
0.1757
0.1556
0.078
0.3644
0.1278
0.1349
69.5283
16.7043
124.9746
6
1.5554
-0.6634
0.7613
2.0485
-0.9311
0.7318
0.0346
0.4528
-0.0681
-0.5803
-0.0287
0.151
0.1642
0.0225
-0.042
0.2246
-0.0903
-0.0105
0.352
0.0079
0.0476
64.9893
-7.3957
125.0103
7
1.1396
-0.2154
0.5561
0.7005
0.178
1.0117
0.0043
-0.0202
-0.12
0.0804
-0.0178
0.0618
0.2558
0.0145
0.0151
0.2152
0.0104
0.0761
0.1852
-0.0042
0.0426
89.226
-11.8931
125.345
8
1.036
-0.2253
-0.5856
0.746
-0.0049
0.7224
0.0062
-0.192
0.1361
0.103
0.089
0.009
-0.2563
0.2107
-0.0387
0.1517
-0.0825
-0.0024
0.1266
-0.0213
0.0436
94.0316
12.0035
125.2487
9
1.4509
-1.1851
-0.2245
1.7187
0.2276
0.3683
0.1253
0.1489
0.2624
-0.225
-0.0935
-0.0981
-0.0105
0.0289
-0.0574
0.0684
0.0507
0.0478
0.0597
-0.015
0.1513
52.0274
30.3693
153.3029
10
2.1083
1.1192
-0.57
0.9801
0.0604
1.0559
-0.1691
0.1898
0.0857
-0.1038
0.0782
-0.048
0.0525
0.1574
0.0599
0.0804
-0.0771
0.1033
0.1224
-0.0031
0.21
51.6285
54.7509
153.2808
11
1.1645
0.7116
-0.4192
1.4255
0.4151
1.1458
0.1482
-0.1738
0.016
0.112
-0.1978
0.0077
-0.1678
0.083
-0.1112
0.0793
-0.0416
0.0661
0.0507
0.0061
0.1516
51.9979
54.3167
178.4905
12
1.5625
-0.826
-0.1158
1.4369
0.7716
0.6609
-0.0585
-0.0705
0.1641
0.1059
0.1323
0.0889
-0.0523
0.0707
-0.0873
0.0772
0.0033
0.0705
0.0609
-0.0111
0.1303
51.8539
30.0026
178.7549
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINC
4
X-RAY DIFFRACTION
4
CHAIND
5
X-RAY DIFFRACTION
5
CHAINE
6
X-RAY DIFFRACTION
6
CHAINF
7
X-RAY DIFFRACTION
7
CHAING
8
X-RAY DIFFRACTION
8
CHAINH
9
X-RAY DIFFRACTION
9
CHAINI
10
X-RAY DIFFRACTION
10
CHAINJ
11
X-RAY DIFFRACTION
11
CHAINK
12
X-RAY DIFFRACTION
12
CHAINL
+
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