Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / meiotic spindle elongation / RAF activation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin D associated events in G1 / regulation of microtubule binding / PKR-mediated signaling / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / Degradation of beta-catenin by the destruction complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / DARPP-32 events / peptidyl-serine dephosphorylation / RHO GTPases Activate Formins / peptidyl-threonine dephosphorylation / Separation of Sister Chromatids / positive regulation of microtubule binding / Platelet sensitization by LDL / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Recruitment of NuMA to mitotic centrosomes / ERK/MAPK targets / Anchoring of the basal body to the plasma membrane / female meiotic nuclear division / AURKA Activation by TPX2 / protein antigen binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase regulator activity / Regulation of PLK1 Activity at G2/M Transition / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of epithelial to mesenchymal transition / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / T cell homeostasis / protein phosphatase activator activity / regulation of G1/S transition of mitotic cell cycle / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / protein dephosphorylation / meiotic cell cycle / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / RAF activation / Spry regulation of FGF signaling / regulation of protein phosphorylation Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / HEAT repeat / HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / HEAT repeat / HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
The biological assembly is a heterotrimer from one A subunit, one B subunit, and one C subunit. There are two heterotrimers in one asymmetric unit. each heterotrimer has one microcystin-LR, PP2A inhibitor.
-
Components
#1: Protein
Serine/threonine-proteinphosphatase2A65kDaregulatorysubunitAalphaisoform / PP2A / subunit A / PR65-alpha isoform / PP2A / subunit A / R1-alpha isoform
Mass: 65392.367 Da / Num. of mol.: 2 / Fragment: Aalpha subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp2r1a / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star References: UniProt: Q76MZ3, protein-serine/threonine phosphatase
#2: Protein
Serine/threonine-proteinphosphatase2A56kDaregulatorysubunitgammaisoform / PP2A / B subunit / B' gamma isoform / PP2A / B subunit / B56 gamma isoform / PP2A / B subunit / ...PP2A / B subunit / B' gamma isoform / PP2A / B subunit / B56 gamma isoform / PP2A / B subunit / PR61 gamma isoform / PP2A / B subunit / R5 gamma isoform / NY-REN-29 antigen
Mass: 48186.934 Da / Num. of mol.: 2 / Fragment: B56gamma1 subunit, residues 30-436 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star References: UniProt: Q13362, protein-serine/threonine phosphatase
#3: Protein
Serine/threonine-proteinphosphatase2Acatalyticsubunitalphaisoform / PP2A-alpha / Replication protein C / RP-C
Mass: 35649.195 Da / Num. of mol.: 2 / Fragment: Calpha subunit / Mutation: D88N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P67775, protein-serine/threonine phosphatase
Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Redundancy: 8.5 % / Av σ(I) over netI: 5.9 / Number: 554144 / Rmerge(I) obs: 0.161 / Χ2: 1.4 / D res high: 3.7 Å / D res low: 50 Å / Num. obs: 65390 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
7.96
50
96
1
0.053
3.077
8.5
6.32
7.96
97.7
1
0.117
1.851
8.6
5.53
6.32
98.4
1
0.187
1.303
8.7
5.02
5.53
98.7
1
0.212
1.204
8.7
4.66
5.02
99.1
1
0.217
1.168
8.7
4.39
4.66
99.3
1
0.256
1.134
8.7
4.17
4.39
99.5
1
0.333
1.092
8.7
3.99
4.17
99.6
1
0.495
1.046
8.7
3.83
3.99
99.8
1
0.68
1.015
8.5
3.7
3.83
99.6
1
0.916
1.001
7.1
Reflection
Resolution: 3.5→50 Å / Num. obs: 76332 / % possible obs: 97.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Diffraction-ID
% possible all
3.5-3.63
4.1
0.905
1
98.1
3.63-3.77
4.3
0.614
1
98.5
3.77-3.94
4.4
0.438
1
98.9
3.94-4.15
4.4
0.297
1
98.9
4.15-4.41
4.4
0.185
1
98.7
4.41-4.75
4.4
0.137
1
97.9
4.75-5.23
4.4
0.118
1
98
5.23-5.98
4.4
0.115
1
96.8
5.98-7.53
4.4
0.094
1
96.1
7.53-50
4.4
0.046
1
93
-
Phasing
Phasing
Method: SAD
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 76221
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
18.19-100
78.2
0.643
518
13.13-18.19
66.2
0.816
886
10.8-13.13
65.4
0.858
1140
9.38-10.8
66.1
0.881
1318
8.41-9.38
65
0.892
1529
7.69-8.41
63.3
0.875
1679
7.13-7.69
65.3
0.855
1835
6.67-7.13
67.3
0.85
1946
6.29-6.67
67.2
0.843
2076
5.97-6.29
68.4
0.852
2227
5.7-5.97
71.7
0.854
2311
5.46-5.7
72.2
0.861
2456
5.24-5.46
71.5
0.869
2529
5.05-5.24
75
0.876
2674
4.88-5.05
76.2
0.883
2731
4.73-4.88
77.1
0.888
2871
4.59-4.73
79.7
0.901
2937
4.46-4.59
86.1
0.894
3007
4.34-4.46
90.7
0.896
3108
4.23-4.34
91.2
0.902
3203
4.13-4.23
90.4
0.902
3288
4.04-4.13
89.6
0.901
3294
3.95-4.04
91.2
0.901
3486
3.87-3.95
88.7
0.904
3516
3.79-3.87
90
0.907
3599
3.71-3.79
89.2
0.907
3603
3.65-3.71
88.7
0.908
3751
3.58-3.65
89.7
0.892
3761
3.5-3.58
90.6
0.775
4942
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHARP
phasing
DM
6
phasing
REFMAC
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.854 / SU B: 59.364 / SU ML: 0.455 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31552
3832
5.1 %
RANDOM
Rwork
0.25681
-
-
-
obs
0.2598
72008
97.48 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 108.538 Å2
Refinement step
Cycle: LAST / Resolution: 3.5→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
19951
0
4
0
19955
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
20389
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.38
1.971
27690
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.269
5
2511
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.351
24.376
914
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
22.445
15
3435
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.513
15
114
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
3190
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
15326
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.235
0.2
11543
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.312
0.2
14144
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.155
0.2
719
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.032
0.2
1
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.271
0.2
43
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.227
0.2
4
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
0.363
1.5
12916
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.671
2
20428
X-RAY DIFFRACTION
r_scbond_it
0.765
3
8308
X-RAY DIFFRACTION
r_scangle_it
1.356
4.5
7262
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3.5→3.588 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.332
253
-
Rwork
0.278
5195
-
obs
-
-
97.92 %
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
1.7024
-0.7702
-0.061
1.4094
-0.1957
0.2101
0.0732
0.4694
-0.4192
-0.6148
-0.1786
0.5373
0.0092
-0.1773
0.1054
0.0529
0.0904
-0.2281
0.1069
-0.269
-0.3051
118.0312
220.9926
98.3446
2
0.89
-0.1591
-0.3709
1.2606
0.4458
1.8055
-0.2379
-0.1023
-0.5066
0.1225
0.0041
0.2632
0.0921
-0.3855
0.2338
-0.5581
-0.122
0.2423
-0.6365
-0.005
-0.2814
166.6063
168.5954
107.2622
3
3.7098
-0.0788
-0.2996
1.7602
-0.2402
3.266
-0.0745
0.333
0.054
-0.3204
0.0391
0.038
0.0248
-0.1442
0.0354
-0.0667
0.2689
-0.2171
-0.1745
-0.1242
-0.1876
114.428
249.235
116.203
4
5.4633
0.6814
-0.0719
4.1511
-0.5067
6.0579
-0.0386
-0.1262
-0.4762
0.3322
-0.108
0.0171
0.4233
0.0498
0.1467
-1.0146
-0.0477
0.2552
-1.5077
-0.3204
-1.2523
194.8149
165.2957
86.1918
5
2.9339
-1.8352
-0.1022
3.4823
0.2217
0.8555
0.1333
-0.0602
0.2818
0.0602
-0.0688
-0.3129
-0.0134
0.2509
-0.0644
0.0643
-0.0644
0.1324
0.0599
-0.0421
-0.1589
195.4888
194.3911
116.4937
6
1.4718
0.1804
-0.2016
5.4423
-1.6328
2.0073
-0.177
-0.1561
0.2922
-0.1848
0.1289
-0.2331
-0.1295
-0.1522
0.0481
-0.0508
0.1295
0.0906
-0.2863
-0.0521
-0.2816
148.4674
227.0913
122.9527
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
7 - 589
7 - 589
2
X-RAY DIFFRACTION
2
D
D
7 - 589
7 - 589
3
X-RAY DIFFRACTION
3
C
C
4 - 309
4 - 309
4
X-RAY DIFFRACTION
4
F
F
4 - 294
4 - 294
5
X-RAY DIFFRACTION
5
E
E
30 - 406
1 - 377
6
X-RAY DIFFRACTION
6
B
B
31 - 406
2 - 377
+
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