DNA double-strand break processing involved in repair via single-strand annealing / BRCA1-C complex / blastocyst hatching / single-stranded DNA endodeoxyribonuclease activity / homologous recombination / DNA strand resection involved in replication fork processing / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / mitotic G2/M transition checkpoint / Defective homologous recombination repair (HRR) due to BRCA1 loss of function ...DNA double-strand break processing involved in repair via single-strand annealing / BRCA1-C complex / blastocyst hatching / single-stranded DNA endodeoxyribonuclease activity / homologous recombination / DNA strand resection involved in replication fork processing / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / mitotic G2/M transition checkpoint / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / transcription repressor complex / meiotic cell cycle / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Meiotic recombination / G1/S transition of mitotic cell cycle / transcription corepressor activity / site of double-strand break / Processing of DNA double-strand break ends / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / Hydrolases; Acting on ester bonds / cell division / intracellular membrane-bounded organelle / DNA repair / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function
DNA endonuclease Ctp1, N-terminal / DNA endonuclease RBBP8-like / Tumour-suppressor protein CtIP N-terminal domain / DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus Similarity search - Domain/homology
RBBP8 / CTBP-INTERACTING PROTEIN / CTIP / RETINOBLASTOMA-BINDING PROTEIN 8 / RBBP-8 / RETINOBLASTOMA- ...CTBP-INTERACTING PROTEIN / CTIP / RETINOBLASTOMA-BINDING PROTEIN 8 / RBBP-8 / RETINOBLASTOMA-INTERACTING PROTEIN AND MYOSIN-LIKE / RIM / SPORULATION IN THE ABSENCE OF SPO11 PROTEIN 2 HOMOLOG / SAE2
Mass: 4512.235 Da / Num. of mol.: 8 / Fragment: TETRAMERISATION DOMAIN, RESIDUES 18-52 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMAT11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 References: UniProt: Q99708, Hydrolases; Acting on ester bonds
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0397 Å / Relative weight: 1
Reflection
Resolution: 1.9→28.98 Å / Num. obs: 20994 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.53 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shell
Resolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.0
refinement
XDS
datareduction
XDS
datascaling
Aimless
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.16 Å / Cor.coef. Fo:Fc: 0.9349 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.492 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.164 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2514
1079
5.15 %
RANDOM
Rwork
0.2122
-
-
-
obs
0.2144
20969
99.4 %
-
Displacement parameters
Biso mean: 49.38 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.1078 Å2
0 Å2
0.4275 Å2
2-
-
-5.4139 Å2
0 Å2
3-
-
-
5.5217 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→20.16 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2267
0
70
137
2474
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4703
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.88
8552
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1107
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
78
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
623
HARMONIC
5
X-RAY DIFFRACTION
t_it
4703
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.35
X-RAY DIFFRACTION
t_other_torsion
14.2
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
279
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
4747
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.9→1.99 Å / Total num. of bins used: 11
Rfactor
Num. reflection
% reflection
Rfree
0.2294
136
4.9 %
Rwork
0.2164
2642
-
all
0.217
2778
-
obs
-
-
99.4 %
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
1.7067
-0.3173
-0.4709
0.8468
-3.0063
13.8012
-0.0751
0.4117
-0.1381
-0.2985
0.1932
-0.2335
0.3318
-0.1157
-0.118
0.2053
-0.0748
0.0848
0.08
-0.0325
-0.2236
3.4807
-1.7288
9.7623
2
2.3703
0.3113
2.0236
2.4515
-0.1582
7.6394
-0.0575
-0.1392
0.0991
0.5208
-0.0601
-0.4378
0.0489
0.1926
0.1176
-0.0524
0.0318
-0.1298
-0.1508
-0.0527
-0.2177
5.0793
2.0162
36.9078
3
0.3807
0.2005
-1.3083
1.55
-1.5864
4.8291
-0.022
-0.0844
-0.0734
-0.0895
0.0374
0.0517
0.4498
-0.2257
-0.0154
-0.0693
-0.0292
-0.0333
0.1211
0.0077
-0.1857
-4.089
-5.4603
41.6799
4
0.9232
-0.2196
2.1618
0.6906
-1.0586
9.5247
0.04
-0.0652
-0.0229
-0.2471
0.0326
0.1167
-0.2366
-0.4973
-0.0727
0.0895
0.0779
-0.0749
0.0776
-0.001
-0.1379
-4.9876
4.8806
11.0018
5
1.6474
-0.6549
-0.9086
0.7689
0.2042
8.6547
-0.0217
-0.3968
-0.0015
0.0193
0.1747
-0.0077
-0.4601
0.4258
-0.153
0.0046
0.0335
-0.0634
0.0697
0.0056
-0.2688
22.6118
-16.1381
35.4284
6
0.9094
0.2972
-0.599
0.4446
0.0719
1.9523
0.0713
0.2117
-0.0411
-0.0842
0.0028
-0.1121
0.1387
0.2058
-0.074
0.1287
0.1529
-0.0984
0.1191
-0.0597
-0.2575
23.4812
-20.8514
11.8281
7
0.5544
0.301
-0.3566
0.8686
-0.931
6.8575
-0.1363
0.1916
-0.0542
-0.4709
0.1406
0.1061
-0.3138
-0.6478
-0.0042
0.2436
0.0312
-0.1349
0.119
-0.0483
-0.2233
14.3363
-13.4918
8.7485
8
0.4081
-0.187
0.2824
0.8057
-0.494
4.4101
0.0036
-0.0944
-0.1149
-0.2434
-0.0986
0.143
0.0797
-0.45
0.095
-0.0289
0.0304
-0.1182
0.0574
-0.0535
-0.1807
13.6081
-23.5621
33.8882
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
+
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