positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / negative regulation of BMP signaling pathway / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / negative regulation of TORC1 signaling / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of ...Details: Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 30.479 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27538
622
4.8 %
RANDOM
Rwork
0.2087
-
-
-
all
0.21177
13247
-
-
obs
0.21177
13133
97.52 %
-
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: 43.342 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.97 Å2
-0 Å2
0 Å2
2-
-
-1.82 Å2
-0 Å2
3-
-
-
0.85 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3600
0
0
40
3640
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
3698
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2549
X-RAY DIFFRACTION
r_angle_refined_deg
1.095
1.975
5023
X-RAY DIFFRACTION
r_angle_other_deg
0.808
3
6270
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.649
5
450
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.352
24.753
162
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.719
15
654
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.739
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
560
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
4022
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
677
X-RAY DIFFRACTION
r_mcbond_it
2.619
2.5
2276
X-RAY DIFFRACTION
r_mcbond_other
0.505
2.5
886
X-RAY DIFFRACTION
r_mcangle_it
4.661
5
3717
X-RAY DIFFRACTION
r_scbond_it
3.513
2.5
1422
X-RAY DIFFRACTION
r_scangle_it
5.951
5
1305
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
A
778
tightpositional
0.02
0.05
2
2
C
990
mediumpositional
0.25
0.5
1
1
A
778
tightthermal
0.45
0.5
2
2
C
990
mediumthermal
0.49
2
LS refinement shell
Resolution: 2.7→2.756 Å / Total num. of bins used: 25
Rfactor
Num. reflection
% reflection
Rfree
0.51
47
-
Rwork
0.307
717
-
obs
-
-
98.58 %
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
0.5165
0.0598
0.6924
1.4066
1.2531
3.2141
0.0264
0.029
-0.0219
0.0688
-0.0369
-0.0557
0.2012
-0.0078
0.0105
0.1293
-0.0039
0.0144
0.0899
0.0268
0.0848
2.2863
19.0461
33.6864
2
1.0249
0.1941
-0.0838
3.1262
0.0599
1.6981
-0.2224
-0.0511
-0.0381
-0.134
0.2316
-0.0582
-0.0331
0.1883
-0.0092
0.0966
0.0155
0.026
0.1149
-0.0037
0.0781
12.0049
50.2918
10.5067
3
1.941
0.0594
0.8408
3.5983
0.1209
4.8786
0.0811
0.0728
-0.0202
0.078
-0.0698
0.0397
-0.0654
-0.0299
-0.0112
0.0175
-0.0127
0.0233
0.0461
-0.0072
0.1027
-0.6131
42.4372
33.0572
4
5.3677
-0.9046
-0.0959
5.2689
-0.929
4.9335
0.0906
0.1105
0.1599
-0.0783
-0.1136
-0.1075
-0.1206
-0.1498
0.023
0.1126
-0.0322
0.0359
0.071
0.0149
0.0705
10.3371
61.8829
-10.3491
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 147
2
X-RAY DIFFRACTION
2
B
1 - 147
3
X-RAY DIFFRACTION
3
C
1 - 73
4
X-RAY DIFFRACTION
4
D
1 - 73
+
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