regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Neddylation / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97903 Å / Relative weight: 1
Reflection
Resolution: 2.8→45 Å / Num. obs: 38647 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.71
Reflection shell
Resolution: 2.8→2.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.97 / % possible all: 96.1
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.0
refinement
XDS
datareduction
XDS
datascaling
BUSTER
TNT
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PVHL54-213-ELOB-ELOC APO STRUCTURE Resolution: 2.8→27.59 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.342 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2358
1960
5.08 %
RANDOM
Rwork
0.1847
-
-
-
obs
0.1873
38613
95.55 %
-
Displacement parameters
Biso mean: 57.68 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.5479 Å2
0 Å2
0 Å2
2-
-
3.5479 Å2
0 Å2
3-
-
-
-7.0957 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→27.59 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9894
0
108
193
10195
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
10260
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.23
14016
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
3305
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
199
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1513
HARMONIC
5
X-RAY DIFFRACTION
t_it
10260
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.1
X-RAY DIFFRACTION
t_other_torsion
21.53
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1408
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
11613
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→2.88 Å / Total num. of bins used: 19
Rfactor
Num. reflection
% reflection
Rfree
0.2918
147
5.03 %
Rwork
0.2039
2773
-
all
0.2084
2920
-
obs
-
-
95.55 %
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
4.8262
-2.1442
-0.9536
2.0079
1.5456
4.1268
-0.0354
-0.3988
-0.2516
0.1457
-0.0709
-0.079
0.2948
0.0505
0.1063
-0.0236
-0.0461
0.0778
-0.0732
0.0955
-0.2159
-17.9508
2.6397
42.9632
2
3.2217
0.4545
-2.8599
3.1432
0.5551
4.1393
0.0317
-0.0006
-0.2571
-0.1798
-0.175
-0.2414
0.1594
-0.0332
0.1433
0.1092
-0.0176
0.1299
-0.1375
0.0109
-0.1543
-14.5036
-1.4737
25.8336
3
0.8358
0.4805
0.5008
7.1814
-3.6426
3.9341
0.0944
0.1389
0.0165
-0.2869
-0.0362
-0.029
-0.0238
-0.0864
-0.0583
0.0717
0.0017
0.255
-0.1878
-0.0437
-0.1962
-7.5029
19.2555
8.9428
4
1.9465
-2.2289
-1.3523
4.2141
1.8249
5.3809
0.1121
-0.7122
0.0809
0.449
-0.0436
0.482
0.7468
-0.4204
-0.0685
0.0065
-0.1332
0.0594
0.0238
0.0286
-0.2811
28.3426
-1.2324
43.8461
5
2.3592
0.6279
-2.8018
3.486
1.0328
6.9258
-0.0041
-0.019
-0.3311
0.0928
-0.1195
0.0221
0.4415
-0.4236
0.1236
0.0538
-0.0892
0.066
-0.1349
0.0172
-0.176
32.1884
-5.2907
26.0554
6
1.4002
-0.4557
-0.5704
4.8175
-0.9528
3.8262
0.1712
-0.0094
-0.0082
-0.3273
-0.0542
0.0691
-0.3196
-0.1044
-0.1171
0.1146
-0.0178
0.1129
-0.1905
-0.0302
-0.204
39.1557
14.3713
8.9643
7
2.0584
-0.9432
-0.5779
2.3486
0.3506
6.588
-0.1989
-0.3088
0.2375
0.3542
0.1483
0.3342
0.4821
-0.3902
0.0506
0.1488
-0.0117
0.1503
-0.0976
0.0484
-0.3116
32.9284
44.0465
43.404
8
1.227
1.4683
-1.1471
2.855
0.3528
5.0467
0.0026
0.111
0.1986
0.0031
-0.0323
0.3897
0.7178
-0.3611
0.0297
0.2513
-0.0386
0.091
-0.1418
0.0317
-0.2529
34.7201
40.595
25.5755
9
1.3696
-0.6528
0.0746
3.3235
-0.7158
1.465
0.1138
0.003
0.0927
-0.4108
-0.1629
-0.073
0.1874
-0.0611
0.0492
0.317
-0.017
0.1267
-0.1755
0.0111
-0.2916
39.3751
61.6085
8.3231
10
3.3891
-2.291
-0.1933
2.666
1.198
5.761
-0.0909
-0.3306
0.2504
0.2491
-0.0153
-0.0251
0.6023
-0.4515
0.1061
0.0634
-0.1103
0.0926
-0.0998
0.0327
-0.276
-14.4682
47.9837
43.0788
11
1.2212
2.2199
-1.4934
4.7122
0.1178
5.8526
0.0416
0.1526
-0.004
-0.1474
-0.1123
0.1569
0.6648
-0.1999
0.0707
0.1625
-0.0638
0.1258
-0.1353
0.0178
-0.1853
-12.3076
44.9036
25.3383
12
1.4101
0.2451
-0.3371
3.2093
-0.9112
2.7943
0.0742
-0.0086
0.0369
-0.3358
-0.1958
-0.0215
0.058
-0.0024
0.1216
0.1602
0.0146
0.2423
-0.2111
-0.0171
-0.2024
-7.2406
65.5569
8.1626
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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