- PDB-2hth: Structural basis for ubiquitin recognition by the human EAP45/ESC... -
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Basic information
Entry
Database: PDB / ID: 2hth
Title
Structural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain
Components
Ubiquitin
Vacuolar protein sorting protein 36
Keywords
PROTEIN TRANSPORT / GLUE domain / PH domain / Protein sorting / viral budding / Ubiquitin complex
Function / homology
Function and homology information
ESCRT II complex / : / : / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein modification process => GO:0036211 / membrane fission / multivesicular body assembly / phosphatidylinositol-3-phosphate binding / Peptide chain elongation / Selenocysteine synthesis ...ESCRT II complex / : / : / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein modification process => GO:0036211 / membrane fission / multivesicular body assembly / phosphatidylinositol-3-phosphate binding / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / HCMV Late Events / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / 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 / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / 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 Similarity search - Function
Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ribosomal L40e family / Ribosomal_L40e ...Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Roll / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Vacuolar protein-sorting-associated protein 36 Similarity search - Component
Biological species
Homo sapiens (human)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.1
1
2
0.9791
1
Reflection
Av σ(I) over netI: 8.1 / Number: 187787 / Rmerge(I) obs: 0.123 / Χ2: 1.01 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 12326 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
6.67
50
99.9
1
0.085
1.023
5.3
6.67
99.9
1
0.102
0.879
4.63
5.3
100
1
0.105
1.065
4.21
4.63
100
1
0.111
1.085
3.91
4.21
100
1
0.139
1.392
3.68
3.91
100
1
0.152
1.408
3.49
3.68
100
1
0.205
1.072
3.34
3.49
100
1
0.254
0.876
3.21
3.34
100
1
0.376
0.685
3.1
3.21
100
1
0.53
0.586
Reflection
Resolution: 2.7→50 Å / Num. obs: 8264 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11
Method to determine structure: SAD / Resolution: 2.7→37.32 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.873 / SU B: 13.718 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP RESIDUES 32-36, 53-57, 74-78 AND 90-103 ARE SET AT ZERO OCCUPANCY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28872
810
9.8 %
RANDOM
Rwork
0.24775
-
-
-
obs
0.25184
7426
97.73 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 56.345 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.73 Å2
0 Å2
0 Å2
2-
-
-1.73 Å2
0 Å2
3-
-
-
3.45 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→37.32 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1640
0
0
0
1640
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1436
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.681
1.953
1930
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.251
5
167
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.972
23.913
69
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.795
15
280
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
224
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1038
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.2
518
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.317
0.2
937
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.148
0.2
33
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
0.199
0.2
12
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
1.032
1.5
877
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.814
2
1385
X-RAY DIFFRACTION
r_scbond_it
2.333
3
601
X-RAY DIFFRACTION
r_scangle_it
3.68
4.5
545
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.37
49
-
Rwork
0.367
440
-
obs
-
-
79.64 %
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
19.634
-16.9771
17.2776
48.4984
-33.2837
31.7127
0.4256
1.1251
0.3466
-2.0371
0.1549
0.0719
0.5117
-0.5583
-0.5804
0.1442
-0.0561
0.1675
0.3623
0
0.6009
-5.3993
-25.0366
-25.8532
2
11.1428
3.0065
1.7129
23.55
-2.6671
7.9247
-0.0635
0.7222
1.6764
-0.2905
0.352
0.4973
-0.8265
-0.4311
-0.2885
0.1873
0.0437
0.1834
0.3439
0.0607
0.638
-4.9871
-18.8278
-22.1207
3
10.611
-4.9379
-2.2412
10.8899
-6.0097
12.4347
-0.6711
-0.5165
0.7323
1.005
0.958
0.2475
-0.6627
-0.6338
-0.2869
0.1711
-0.0085
0.1243
0.1263
0.0068
0.6151
-4.5547
-22.1567
-14.1221
4
14.7253
-12.0584
-12.7211
16.9704
8.7893
54.8173
-0.3704
-1.2615
1.5901
0.6208
0.9662
-0.1425
-0.9035
2.3249
-0.5958
0.1854
-0.1288
-0.0359
0.386
-0.0789
0.8471
4.719
-24.0905
-16.9787
5
19.7679
-0.8298
4.0061
14.4189
-3.1264
1.4202
-0.5057
1.2566
1.0785
-0.8916
-0.206
-0.7966
-0.7334
1.0542
0.7118
0.3623
-0.1263
0.1596
0.3249
0.155
0.7623
6.729
-17.3533
-25.1469
6
9.48
-4.444
1.2532
11.2689
-5.8792
7.6055
0.3157
1.2911
0.7637
-0.7296
-0.5377
-0.3306
-0.3848
0.3145
0.222
0.1396
-0.0147
0.1327
0.2709
0.0627
0.5364
1.0983
-20.9967
-26.2825
7
5.9458
-0.1076
-1.8299
6.8719
4.2756
11.2208
-0.1844
-0.1297
-0.5964
0.3415
-0.3363
0.2974
0.4668
-0.4607
0.5207
0.2069
-0.0006
0.0157
0.1302
0.0043
0.6369
18.3435
-43.9012
-33.3588
8
7.9222
-0.0113
-1.2208
8.6676
7.6621
6.9583
-0.5329
-0.4755
-0.7273
1.1487
0.5099
-0.1685
0.9604
-0.2136
0.0229
0.2665
0.0373
-0.0031
0.1906
0.0089
0.6573
18.3896
-42.119
-29.7728
9
4.0699
-0.2853
-0.7193
6.3016
4.4173
5.3232
-0.1245
-0.4479
-0.5231
0.4937
0.0356
-0.1142
0.766
0.1438
0.0889
0.1617
-0.0435
0.0765
0.2586
0.0714
0.5299
15.7534
-39.4118
-27.1543
10
13.7454
-9.2369
-4.3611
7.8278
2.9229
9.6719
0.348
0.1735
-1.1805
0.0254
-0.2911
0.7587
0.3725
-0.9308
-0.0569
0.2663
-0.059
0.0605
0.2199
0.0465
0.6263
11.9839
-37.392
-22.1819
11
12.7785
3.2136
-1.0869
20.1873
-2.2771
2.7771
-0.3526
-0.6829
-0.2631
0.9876
0.0945
-1.1637
0.1107
0.5612
0.2581
0.1396
0.0657
-0.0364
0.2017
-0.0131
0.4271
25.243
-33.6986
-26.2715
12
29.7743
-4.2892
8.2628
8.3266
-12.7165
19.5273
-0.6613
0.7767
0.1505
-1.1114
0.7561
0.9383
0.6111
-0.4472
-0.0948
0.1483
-0.0171
-0.1132
0.1884
0.0252
0.6013
14.3316
-29.3624
-36.305
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
1 - 8
1 - 8
2
X-RAY DIFFRACTION
2
A
A
9 - 26
9 - 26
3
X-RAY DIFFRACTION
3
A
A
27 - 38
27 - 38
4
X-RAY DIFFRACTION
4
A
A
39 - 44
39 - 44
5
X-RAY DIFFRACTION
5
A
A
45 - 55
45 - 55
6
X-RAY DIFFRACTION
6
A
A
56 - 73
56 - 73
7
X-RAY DIFFRACTION
7
B
B
5 - 29
7 - 31
8
X-RAY DIFFRACTION
8
B
B
30 - 47
32 - 49
9
X-RAY DIFFRACTION
9
B
B
48 - 83
50 - 85
10
X-RAY DIFFRACTION
10
B
B
84 - 112
86 - 114
11
X-RAY DIFFRACTION
11
B
B
113 - 124
115 - 126
12
X-RAY DIFFRACTION
12
B
B
125 - 131
127 - 133
+
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