- PDB-4ibe: Ebola virus VP35 bound to small molecule -
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Basic information
Entry
Database: PDB / ID: 4ibe
Title
Ebola virus VP35 bound to small molecule
Components
Polymerase cofactor VP35
Keywords
TRANSCRIPTION/TRANSCRIPTION inhibitor / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / interferon inhibitor domain / TRANSCRIPTION-TRANSCRIPTION inhibitor complex
Function / homology
Function and homology information
suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / RNA binding Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979237 Å / Relative weight: 1
Reflection
Resolution: 1.95→50 Å / Num. obs: 17475 / % possible obs: 93.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Diffraction-ID
% possible all
1.95-1.98
3.3
0.862
1
94.5
1.98-2.02
3.5
0.776
1
95.1
2.02-2.06
3.7
0.673
1
96.5
2.06-2.1
3.9
0.582
1
95.8
2.1-2.15
4.2
0.538
1
95.1
2.15-2.2
4.3
0.491
1
96.1
2.2-2.25
4.4
0.431
1
95.2
2.25-2.31
4.5
0.386
1
94.8
2.31-2.38
4.6
0.334
1
94.5
2.38-2.46
4.6
0.285
1
94.7
2.46-2.54
4.6
0.251
1
93.8
2.54-2.65
4.6
0.202
1
94.1
2.65-2.77
4.6
0.176
1
93.6
2.77-2.91
4.7
0.137
1
92.6
2.91-3.1
4.7
0.119
1
93.7
3.1-3.33
4.7
0.095
1
92.7
3.33-3.67
4.8
0.074
1
92.2
3.67-4.2
4.8
0.058
1
91.7
4.2-5.29
4.7
0.052
1
90.6
5.29-50
4.9
0.052
1
86
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
PHENIX
1.8.1_1168
refinement
SCALEPACK
datascaling
MOLREP
phasing
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
HKL-3000
datacollection
DENZO
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.502 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2719 / σ(F): 1.36 / Phase error: 28.15 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Rfree
0.2326
1498
9.93 %
Rwork
0.1825
-
-
obs
0.1874
15087
80.23 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 26.7313 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→48.502 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1917
0
68
163
2148
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
2085
X-RAY DIFFRACTION
f_angle_d
1.2
2843
X-RAY DIFFRACTION
f_dihedral_angle_d
16.467
821
X-RAY DIFFRACTION
f_chiral_restr
0.066
306
X-RAY DIFFRACTION
f_plane_restr
0.006
376
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9358-1.9983
0.2765
81
0.205
596
X-RAY DIFFRACTION
40
1.9983-2.0697
0.264
77
0.2062
836
X-RAY DIFFRACTION
55
2.0697-2.1526
0.2148
115
0.198
1022
X-RAY DIFFRACTION
68
2.1526-2.2505
0.2638
134
0.2017
1176
X-RAY DIFFRACTION
77
2.2505-2.3692
0.2389
141
0.1947
1315
X-RAY DIFFRACTION
87
2.3692-2.5176
0.2855
142
0.1969
1434
X-RAY DIFFRACTION
93
2.5176-2.712
0.24
145
0.2019
1448
X-RAY DIFFRACTION
94
2.712-2.9849
0.2472
177
0.1884
1426
X-RAY DIFFRACTION
93
2.9849-3.4167
0.2204
144
0.1722
1445
X-RAY DIFFRACTION
93
3.4167-4.3043
0.1989
175
0.1532
1431
X-RAY DIFFRACTION
92
4.3043-48.5175
0.2383
167
0.1866
1460
X-RAY DIFFRACTION
89
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
3.4063
2.9993
-2.5386
7.4819
-0.986
2.704
-0.4314
0.753
-0.9429
-0.4743
0.297
0.2742
0.4408
-0.1959
0.015
0.2629
-0.0057
-0.0253
0.2471
-0.0528
0.2628
1.9543
22.5283
-12.2789
2
6.1445
-1.5183
0.0556
0.9682
-0.2983
2.5041
0.0486
0.2569
-0.1697
0.055
0.0186
0.1018
-0.171
-0.0252
-0.0224
0.115
-0.0238
0.0061
0.1223
-0.0261
0.1029
3.2349
29.1187
-8.4005
3
5.1565
1.4843
-4.7451
2.232
-0.7289
5.1358
0.1654
0.6035
0.7362
-0.2038
0.2557
0.2516
-0.5567
0.0138
-0.4167
0.1786
-0.0379
-0.0079
0.2107
0.04
0.2322
7.966
36.8719
-10.0172
4
9.4241
-5.2123
1.2148
7.8159
-2.7018
5.0076
-0.1507
-0.5254
-0.2595
0.6936
0.0952
0.1247
0.2865
-0.0635
0.0416
0.2674
-0.1033
0.0456
0.2631
-0.0298
0.172
5.0507
27.8885
5.2617
5
5.1575
2.0724
2.4132
3.5628
-0.141
6.7759
0.0049
-0.0774
0.3458
0.6647
-0.0991
-0.1319
0.3094
0.1818
0.1519
0.2228
-0.0242
-0.0048
0.2093
0.0104
0.1168
14.0871
31.0686
7.0997
6
5.7959
-1.5917
2.1795
8.7246
-5.396
3.9413
0.0627
-0.3574
0.0471
0.8352
0.1214
0.3761
-0.2045
-0.4975
-0.1753
0.2818
-0.0501
0.0525
0.2713
-0.0658
0.1383
9.2789
30.0227
8.4818
7
6.5595
-4.6543
0.8015
6.3978
-0.4532
5.584
0.1898
0.4256
-0.2125
0.1614
-0.2541
-0.1927
0.3864
0.1488
0.0749
0.2356
0.0291
-0.0379
0.1954
0.0502
0.2408
-1.8081
21.782
34.8772
8
6.4959
0.5706
-0.0056
1.5787
1.4491
4.3647
-0.0172
0.0522
-0.3084
-0.0271
0.0591
-0.109
-0.0151
0.1618
-0.0356
0.1144
0.0225
-0.0046
0.0662
0.0402
0.1355
-3.2336
28.3517
31.1043
9
6.8466
0.1035
-3.6599
0.8979
0.3172
6.1118
0.1127
-0.5938
0.4853
0.0325
0.0544
-0.1552
-0.3017
0.2328
-0.2147
0.1188
0.0277
0.0138
0.0956
-0.0244
0.2098
-4.6866
37.1473
30.0396
10
5.6802
3.1479
3.2337
7.9553
4.3897
4.9175
-0.3435
1.0584
-0.0654
-0.3573
-0.0877
0.0224
0.0059
0.1497
0.0708
0.2611
-0.0183
0.0344
0.1746
-0.1183
0.1519
-9.2412
20.8706
14.1439
11
4.614
-5.5753
1.233
8.4732
2.3834
8.9168
0.24
-0.5885
-0.3569
0.3848
-0.2239
1.2419
0.936
-0.6382
0.0816
0.1978
-0.0835
0.01
0.3833
0.0265
0.2965
-19.0108
24.1335
20.2294
12
5.9145
5.9944
1.6667
8.3326
0.2657
2.0833
0.0523
-0.2042
0.581
0.0487
-0.1208
0.3299
-0.6238
0.1714
0.2187
0.2325
-0.0098
0.0076
0.1897
0.0109
0.2691
-10.2825
36.1679
12.8272
13
6.495
0.5882
1.0326
5.0467
4.171
3.555
0.1351
0.1922
0.0798
-0.42
0.0421
-0.1818
-0.3588
-0.1463
-0.2529
0.2237
0.005
0.0226
0.1657
0.0553
0.1667
-9.2691
29.9328
14.6309
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid218through231 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid232through269 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid270through283 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid284through304 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid305through319 )
6
X-RAY DIFFRACTION
6
chain 'A' and (resid320through340 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid217through231 )
8
X-RAY DIFFRACTION
8
chain 'B' and (resid232through268 )
9
X-RAY DIFFRACTION
9
chain 'B' and (resid269through292 )
10
X-RAY DIFFRACTION
10
chain 'B' and (resid293through304 )
11
X-RAY DIFFRACTION
11
chain 'B' and (resid305through310 )
12
X-RAY DIFFRACTION
12
chain 'B' and (resid311through319 )
13
X-RAY DIFFRACTION
13
chain 'B' and (resid320through340 )
+
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