formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / proline-rich region binding / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / lysosomal transport / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / progesterone receptor signaling pathway / protein K63-linked ubiquitination / phosphoserine residue binding / regulation of macroautophagy / beta-2 adrenergic receptor binding / ubiquitin ligase complex / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ubiquitin binding / regulation of membrane potential / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / positive regulation of protein catabolic process / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / protein domain specific binding / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function
Resolution: 1.8→27.23 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.436 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2086
1357
5.1 %
RANDOM
Rwork
0.16852
-
-
-
obs
0.17056
25255
94.78 %
-
all
-
26612
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 30.718 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.24 Å2
-0.4 Å2
0.41 Å2
2-
-
-1.26 Å2
-0.49 Å2
3-
-
-
0.84 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→27.23 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2330
0
2
221
2553
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2387
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.456
1.978
3251
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.818
5
290
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.155
23.019
106
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.661
15
395
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.397
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
372
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1811
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.2
914
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.312
0.2
1591
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.138
0.2
180
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.115
0.2
3
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.242
0.2
55
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.183
0.2
15
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
1.767
3
1512
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.383
4
2395
X-RAY DIFFRACTION
r_scbond_it
3.418
5
990
X-RAY DIFFRACTION
r_scangle_it
4.852
7
856
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.8→1.85 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.29
90
-
Rwork
0.212
1446
-
obs
-
-
72.28 %
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
9.8663
9.9684
2.7717
20.4287
3.2906
0.8019
-0.2492
0.6049
-0.5439
-0.3118
0.4639
-1.6196
-0.1463
0.398
-0.2147
0.0801
-0.0366
0.0895
0.1308
-0.0174
0.244
-2.2542
27.7556
-2.8359
2
5.4025
-0.4376
0.2412
8.5501
1.3695
43.3586
0.3988
0.3563
0.1665
-0.8965
0.2114
0.1182
-0.4775
-0.7543
-0.6101
0.1357
0.0156
-0.0036
0.0614
0.017
0.0962
-13.3531
28.0867
-3.1284
3
0.9351
1.0609
0.0396
5.8387
2.2891
3.196
0.0377
-0.2672
-0.107
0.886
0.0471
-0.134
0.3676
0.1112
-0.0848
0.2021
0.0374
-0.0314
0.1666
0.0086
0.0772
-10.7567
20.2651
14.5247
4
3.4996
-0.1385
1.0597
6.5794
4.0207
7.4393
0.0154
0.1397
-0.2561
-0.0201
0.1986
-0.2447
0.0737
0.0671
-0.214
0.0458
-0.0026
0.0133
0.0649
0.0109
0.0697
-9.0053
15.7624
2.9736
5
2.2245
0.3305
0.3245
4.2539
1.6107
3.4382
0.0451
-0.1891
-0.0119
0.3541
0.0614
-0.1542
0.1642
0.0185
-0.1064
0.072
0.0109
-0.0044
0.0807
-0.0032
0.0854
-10.6059
21.8579
9.5613
6
12.9042
0.0816
2.9863
7.5482
-0.967
6.2813
0.202
-0.8965
-0.8492
1.1314
-0.1728
-1.123
0.4518
0.3149
-0.0292
0.3471
0.0136
-0.1635
0.1223
0.0969
0.2507
-7.161
12.1311
17.8991
7
3.6411
-2.1778
-1.4473
4.5822
3.8856
4.5436
0.1993
0.1759
0.6615
-0.5897
-0.2213
0.2212
-0.9802
-0.4026
0.022
0.2584
0.1019
-0.0519
0.1903
0.048
0.2512
-19.2723
33.0504
2.0793
8
3.6268
-2.8733
2.3476
24.9577
0.7913
1.8295
0.4072
-0.1308
-0.4783
1.2664
-0.3857
0.8829
0.3
-0.2219
-0.0215
0.1911
-0.0661
0.098
0.1549
0.0166
0.0861
-19.179
15.2103
15.8131
9
2.3319
-1.8065
3.1682
15.9895
1.6664
5.4684
0.0868
-0.3629
-0.1089
1.688
0.0709
0.5851
0.8292
-0.7127
-0.1577
0.3727
-0.0866
0.1154
0.1871
0.0025
0.08
-18.239
18.5446
19.2248
10
10.4952
-3.2425
5.7751
2.4884
3.2263
20.066
0.0129
0.2086
0.0672
-0.2674
-0.121
0.1712
-1.1008
-0.4855
0.1082
0.1864
0.0762
-0.0264
0.0469
0.0005
0.0889
-16.8363
30.8663
-0.1951
11
12.6498
9.4965
1.7568
7.2326
1.7804
2.3061
0.006
0.4334
-0.6624
-0.0974
0.1704
-0.3645
0.4777
0.108
-0.1764
0.1108
-0.0219
0.0213
0.0542
-0.0147
0.2453
14.1823
-10.4262
0.0983
12
17.2343
-9.5009
10.0403
7.1863
-5.4316
11.4676
-0.163
-0.1369
-0.3149
0.416
0.1605
0.1206
0.1368
0.1227
0.0024
0.1125
-0.0108
0.0381
0.0536
0.0532
0.1323
12.9593
-2.8526
8.0085
13
3.0812
0.2353
0.5627
2.6383
-1.1554
3.699
-0.1307
0.3284
0.0402
-0.192
0.0833
0.1774
-0.1767
-0.2322
0.0474
0.0853
0.0015
-0.0076
0.1455
-0.0453
0.1057
0.9739
10.6863
-14.2809
14
12.01
3.0065
6.9774
4.8602
4.3205
7.4143
0.1424
0.2284
-0.421
0.1632
0.056
-0.3
0.1622
0.315
-0.1985
0.0704
-0.0003
0.0282
0.0937
0.006
0.1335
20.4054
4.2644
-1.8591
15
5.2245
-2.5246
1.8869
5.076
-2.7612
5.1495
-0.0609
0.0661
-0.5334
-0.0001
0.1221
0.2059
0.0835
-0.315
-0.0612
0.0344
-0.0339
0.0234
0.0958
-0.0578
0.1396
1.3352
2.6906
-9.7907
16
3.0957
0.5999
0.729
8.1927
-1.8661
2.7442
-0.0381
-0.241
-0.1904
0.3437
-0.0669
-0.303
-0.0205
0.1081
0.105
0.0652
0.0017
0.0165
0.0941
0.0342
0.1551
16.858
2.2044
5.1546
17
1.4384
-1.0131
0.4998
1.9824
1.7887
7.3546
-0.0791
0.1902
0.0108
-0.2544
-0.1239
0.0399
-0.258
-0.0131
0.203
0.1119
-0.0296
0.0048
0.1344
-0.0278
0.1022
9.6935
10.2641
-16.4629
18
2.7788
-1.4807
-0.7216
4.3551
-4.2476
8.0116
-0.2955
-0.3956
-0.1546
0.4173
0.3943
0.4031
0.0225
-0.6839
-0.0987
0.143
0.0088
0.0662
0.237
0.0178
0.1219
8.6094
5.191
9.4763
19
17.7213
7.9317
-10.8236
5.3803
-4.5768
10.3105
-0.0705
-1.1229
-0.2026
0.2563
-0.2288
-0.1127
-0.2378
0.649
0.2993
0.0613
0.0553
0.0131
0.1336
-0.0136
0.0864
4.8054
12.6626
0.2816
20
3.6703
-0.8059
0.7059
1.5564
-0.1022
2.5
0.1227
-0.0082
-0.0433
0.0491
-0.0916
0.134
-0.218
0.1023
-0.0311
0.0619
0.0108
0.0335
0.1041
-0.022
0.0857
6.4024
10.5435
-1.781
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
102 - 114
3 - 15
2
X-RAY DIFFRACTION
2
A
A
115 - 124
16 - 25
3
X-RAY DIFFRACTION
3
A
A
125 - 149
26 - 50
4
X-RAY DIFFRACTION
4
A
A
150 - 164
51 - 65
5
X-RAY DIFFRACTION
5
A
A
165 - 195
66 - 96
6
X-RAY DIFFRACTION
6
A
A
196 - 207
97 - 108
7
X-RAY DIFFRACTION
7
A
A
208 - 225
109 - 126
8
X-RAY DIFFRACTION
8
A
A
226 - 237
127 - 138
9
X-RAY DIFFRACTION
9
A
A
238 - 246
139 - 147
10
X-RAY DIFFRACTION
10
A
A
247 - 252
148 - 153
11
X-RAY DIFFRACTION
11
B
B
102 - 114
3 - 15
12
X-RAY DIFFRACTION
12
B
B
115 - 124
16 - 25
13
X-RAY DIFFRACTION
13
B
B
125 - 144
26 - 45
14
X-RAY DIFFRACTION
14
B
B
145 - 158
46 - 59
15
X-RAY DIFFRACTION
15
B
B
159 - 176
60 - 77
16
X-RAY DIFFRACTION
16
B
B
177 - 188
78 - 89
17
X-RAY DIFFRACTION
17
B
B
189 - 205
90 - 106
18
X-RAY DIFFRACTION
18
B
B
206 - 223
107 - 124
19
X-RAY DIFFRACTION
19
B
B
224 - 234
125 - 135
20
X-RAY DIFFRACTION
20
B
B
235 - 252
136 - 153
+
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