negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / apoptotic process in bone marrow cell / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / metanephros development / neuron maturation / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / fertilization / negative regulation of ossification / negative regulation of B cell apoptotic process / response to UV-B / regulation of mitochondrial membrane permeability / response to iron ion / negative regulation of protein localization to plasma membrane / regulation of growth / calcium ion transport into cytosol / channel activity / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / Bcl-2 family protein complex / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / organ growth / digestive tract morphogenesis / branching involved in ureteric bud morphogenesis / response to cycloheximide / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / : / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / hepatocyte apoptotic process / pore complex / positive regulation of smooth muscle cell migration / B cell proliferation / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / regulation of calcium ion transport / B cell homeostasis / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress Similarity search - Function
Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site ...Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily Similarity search - Domain/homology
Resolution: 1.998→37.429 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.25 Details: Authors state that the diffraction data were ellipsoidally truncated after 2.7 angstrom. Two copies of BCL-2 and S55746 are present in the assymetric unit. The model from chain A is the ...Details: Authors state that the diffraction data were ellipsoidally truncated after 2.7 angstrom. Two copies of BCL-2 and S55746 are present in the assymetric unit. The model from chain A is the preferred chain for analysis as the electron density for chain C is of poorer quality.
Rfactor
Num. reflection
% reflection
Rfree
0.2666
816
4.95 %
Rwork
0.2167
-
-
obs
0.2193
16500
74.32 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 1.998→37.429 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2288
0
106
15
2409
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
2471
X-RAY DIFFRACTION
f_angle_d
0.543
3353
X-RAY DIFFRACTION
f_dihedral_angle_d
13.999
1463
X-RAY DIFFRACTION
f_chiral_restr
0.038
327
X-RAY DIFFRACTION
f_plane_restr
0.004
507
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9981-2.1232
0.4024
42
0.2936
941
X-RAY DIFFRACTION
27
2.1232-2.2872
0.3655
95
0.2793
1780
X-RAY DIFFRACTION
51
2.2872-2.5173
0.3189
129
0.2591
2533
X-RAY DIFFRACTION
72
2.5173-2.8814
0.355
176
0.2649
3362
X-RAY DIFFRACTION
96
2.8814-3.6298
0.2878
185
0.2349
3499
X-RAY DIFFRACTION
100
3.6298-37.4359
0.2193
189
0.1824
3569
X-RAY DIFFRACTION
100
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
1.6656
-0.1732
0.4971
1.8838
-1.9728
3.205
-0.0139
-0.0414
0.2867
0.8516
-0.0651
0.1352
-0.7917
-0.0163
-0.0892
0.8213
-0.1926
-0.0382
0.3347
0.0376
0.2966
23.3349
5.8981
11.259
2
2.3841
0.6135
-1.0329
0.813
0.1518
1.3638
0.2917
-0.2656
0.3502
0.2369
0.0627
0.1923
-0.5173
-0.132
2.3863
0.7715
0.2288
0.2519
0.3371
0.0435
0.2229
10.9032
8.9583
6.4604
3
2.3711
0.2999
1.5841
2.2285
-2.0683
3.4591
0.3579
0.1407
-0.484
0.1961
-0.1102
-0.6518
0.0527
-0.0936
-0.1001
0.5808
0.0497
0.1859
1.1147
0.2587
1.0042
4.2627
-6.2165
10.8434
4
2.1707
-1.3113
2.2199
3.7079
-4.1367
5.7134
-0.1761
0.2406
0.0525
-0.8025
0.2362
0.4824
0.5223
-0.1283
-0.3059
0.5113
-0.065
-0.0688
0.3211
0.0092
0.2265
16.5565
-10.3357
2.1359
5
1.0274
-0.1073
0.1934
1.8776
-1.7525
3.7052
0.1734
-0.1218
0.1316
0.1229
0.0216
0.1257
0.0346
0.0383
-0.0921
0.3202
-0.0365
0.0211
0.2172
0.0321
0.13
19.4565
0.8011
2.3879
6
0.1825
0.0858
0.3291
0.7013
-0.3874
1.0148
-0.1227
-0.4099
-0.2551
-0.0701
0.1718
-0.3615
0.3572
0.5121
0.6839
0.0266
0.1108
0.0423
0.2195
-0.0722
0.4024
27.0846
-36.7333
21.0507
7
3.5734
-3.3748
-1.53
5.9727
0.3454
2.3975
-0.3656
-0.3686
-0.5689
0.7056
0.1356
0.3357
-0.4435
-0.1811
-0.0449
0.4208
0.0245
-0.2176
0.2705
0.0666
0.5209
23.9635
-39.9776
34.1526
8
1.3954
0.1406
0.252
1.6081
-1.8103
2.2193
0.5251
0.3109
-0.2761
0.4736
0.4318
0.2352
0.027
0.0669
-0.2469
1.1385
0.143
0.0673
0.8652
0.1097
0.5667
16.7083
-24.9055
36.1925
9
0.7267
-0.3313
0.9041
0.9648
-1.3161
2.1473
-0.103
-0.1729
0.1325
1.088
0.1804
-0.3758
-0.533
-0.1164
0.2796
0.4587
0.0721
-0.2128
0.3443
-0.0117
0.3532
29.0207
-24.6614
31.394
10
0.6995
-0.7995
1.2415
1.3507
-1.4625
2.1917
0.164
0.3347
-0.159
-0.0848
-0.2488
-0.4728
0.3996
0.5412
0.0836
0.224
0.0733
-0.1013
0.2965
-0.0333
0.4055
35.0954
-33.1483
29.7811
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid9through50 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid51through66 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid67through77 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid78through102 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid103through162 )
6
X-RAY DIFFRACTION
6
chain 'C' and (resid10through50 )
7
X-RAY DIFFRACTION
7
chain 'C' and (resid51through66 )
8
X-RAY DIFFRACTION
8
chain 'C' and (resid67through77 )
9
X-RAY DIFFRACTION
9
chain 'C' and (resid78through122 )
10
X-RAY DIFFRACTION
10
chain 'C' and (resid123through162 )
+
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