[English] 日本語
Yorodumi
- PDB-3i6w: Structure and Activation Mechanism of the CHK2 DNA-Damage Checkpo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i6w
TitleStructure and Activation Mechanism of the CHK2 DNA-Damage Checkpoint Kinase
ComponentsSerine/threonine-protein kinase Chk2
KeywordsTRANSFERASE / Ser/Thr protein kinase / FHA domain / ATP-binding / Cell cycle / Disease mutation / Kinase / Li-Fraumeni syndrome / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / Serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of anoikis / mitotic DNA damage checkpoint signaling / response to glycoside / cellular response to bisphenol A / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / thymocyte apoptotic process / cellular response to stress / regulation of protein catabolic process / negative regulation of DNA damage checkpoint ...positive regulation of anoikis / mitotic DNA damage checkpoint signaling / response to glycoside / cellular response to bisphenol A / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / thymocyte apoptotic process / cellular response to stress / regulation of protein catabolic process / negative regulation of DNA damage checkpoint / replicative senescence / signal transduction in response to DNA damage / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / cellular response to gamma radiation / PML body / Regulation of TP53 Activity through Methylation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / cellular response to xenobiotic stimulus / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Chk2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsPavletich, N.P.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure and activation mechanism of the CHK2 DNA damage checkpoint kinase.
Authors: Cai, Z. / Chehab, N.H. / Pavletich, N.P.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase Chk2
B: Serine/threonine-protein kinase Chk2
C: Serine/threonine-protein kinase Chk2
D: Serine/threonine-protein kinase Chk2
E: Serine/threonine-protein kinase Chk2
F: Serine/threonine-protein kinase Chk2
G: Serine/threonine-protein kinase Chk2
H: Serine/threonine-protein kinase Chk2


Theoretical massNumber of molelcules
Total (without water)406,7208
Polymers406,7208
Non-polymers00
Water00
1
A: Serine/threonine-protein kinase Chk2
B: Serine/threonine-protein kinase Chk2


Theoretical massNumber of molelcules
Total (without water)101,6802
Polymers101,6802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-14 kcal/mol
Surface area37180 Å2
MethodPISA
2
C: Serine/threonine-protein kinase Chk2
D: Serine/threonine-protein kinase Chk2


Theoretical massNumber of molelcules
Total (without water)101,6802
Polymers101,6802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-14 kcal/mol
Surface area37200 Å2
MethodPISA
3
E: Serine/threonine-protein kinase Chk2
F: Serine/threonine-protein kinase Chk2


Theoretical massNumber of molelcules
Total (without water)101,6802
Polymers101,6802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-12 kcal/mol
Surface area36970 Å2
MethodPISA
4
G: Serine/threonine-protein kinase Chk2
H: Serine/threonine-protein kinase Chk2


Theoretical massNumber of molelcules
Total (without water)101,6802
Polymers101,6802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-16 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.200, 114.700, 123.000
Angle α, β, γ (deg.)84.10, 81.20, 80.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H
13A
23C
33E
43G
14B
24D
34F
44H
15A
25B
35C
45D
55E
65F
75G
85H
16B
26D
36F
46H
17B
27D
37F
47H
18A
28C
38E
48G
19A
29B
39C
49D
59E
69F
79G
89H

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROTHRTHRAA92 - 20523 - 136
211PROPROTHRTHRBB92 - 20523 - 136
311PROPROTHRTHRCC92 - 20523 - 136
411PROPROTHRTHRDD92 - 20523 - 136
511PROPROTHRTHREE92 - 20523 - 136
611PROPROTHRTHRFF92 - 20523 - 136
711PROPROTHRTHRGG92 - 20523 - 136
811PROPROTHRTHRHH92 - 20523 - 136
112VALVALVALVALAA206 - 211137 - 142
212VALVALVALVALBB206 - 211137 - 142
312VALVALVALVALCC206 - 211137 - 142
412VALVALVALVALDD206 - 211137 - 142
512VALVALVALVALEE206 - 211137 - 142
612VALVALVALVALFF206 - 211137 - 142
712VALVALVALVALGG206 - 211137 - 142
812VALVALVALVALHH206 - 211137 - 142
113TYRTYRLEULEUAA212 - 226143 - 157
213TYRTYRLEULEUCC212 - 226143 - 157
313TYRTYRLEULEUEE212 - 226143 - 157
413TYRTYRLEULEUGG212 - 226143 - 157
123GLUGLULYSLYSAA233 - 253164 - 184
223GLUGLULYSLYSCC233 - 253164 - 184
323GLUGLULYSLYSEE233 - 253164 - 184
423GLUGLULYSLYSGG233 - 253164 - 184
133LEULEUGLUGLUAA268 - 305199 - 236
233LEULEUGLUGLUCC268 - 305199 - 236
333LEULEUGLUGLUEE268 - 305199 - 236
433LEULEUGLUGLUGG268 - 305199 - 236
114TYRTYRLEULEUBB212 - 226143 - 157
214TYRTYRLEULEUDD212 - 226143 - 157
314TYRTYRLEULEUFF212 - 226143 - 157
414TYRTYRLEULEUHH212 - 226143 - 157
124GLUGLULYSLYSBB233 - 253164 - 184
224GLUGLULYSLYSDD233 - 253164 - 184
324GLUGLULYSLYSFF233 - 253164 - 184
424GLUGLULYSLYSHH233 - 253164 - 184
134LEULEUGLUGLUBB268 - 305199 - 236
234LEULEUGLUGLUDD268 - 305199 - 236
334LEULEUGLUGLUFF268 - 305199 - 236
434LEULEUGLUGLUHH268 - 305199 - 236
115GLYGLYASPASPAA306 - 368237 - 299
215GLYGLYASPASPBB306 - 368237 - 299
315GLYGLYASPASPCC306 - 368237 - 299
415GLYGLYASPASPDD306 - 368237 - 299
515GLYGLYASPASPEE306 - 368237 - 299
615GLYGLYASPASPFF306 - 368237 - 299
715GLYGLYASPASPGG306 - 368237 - 299
815GLYGLYASPASPHH306 - 368237 - 299
116PHEPHEARGARGBB369 - 382300 - 313
216PHEPHEARGARGDD369 - 382300 - 313
316PHEPHEARGARGFF369 - 382300 - 313
416PHEPHEARGARGHH369 - 382300 - 313
117PROPROVALVALBB388 - 397319 - 328
217PROPROVALVALDD388 - 397319 - 328
317PROPROVALVALFF388 - 397319 - 328
417PROPROVALVALHH388 - 397319 - 328
118PROPROVALVALAA388 - 397319 - 328
218PROPROVALVALCC388 - 397319 - 328
318PROPROVALVALEE388 - 397319 - 328
418PROPROVALVALGG388 - 397319 - 328
119ALAALAGLUGLUAA402 - 501333 - 432
219ALAALAGLUGLUBB402 - 501333 - 432
319ALAALAGLUGLUCC402 - 501333 - 432
419ALAALAGLUGLUDD402 - 501333 - 432
519ALAALAGLUGLUEE402 - 501333 - 432
619ALAALAGLUGLUFF402 - 501333 - 432
719ALAALAGLUGLUGG402 - 501333 - 432
819ALAALAGLUGLUHH402 - 501333 - 432

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
Detailstransient dimer, four copies of dimer in asymmetric unit

-
Components

#1: Protein
Serine/threonine-protein kinase Chk2 / Cds1


Mass: 50839.945 Da / Num. of mol.: 8 / Fragment: residues 70-512 / Mutation: K249A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK2, CHK2, RAD53 / Production host: Escherichia coli (E. coli)
References: UniProt: O96017, non-specific serine/threonine protein kinase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0 and well bufffer (100 mM NaHepes, 300 mM Ammonium ...Details: 1:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0 and well bufffer (100 mM NaHepes, 300 mM Ammonium Tartrate, 22% PEG 3350, pH 7.0). Crystals were flash frozen in crystallization buffer supplemented with 16-20% (v/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.03944
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03944 Å / Relative weight: 1
ReflectionResolution: 3.25→30 Å / Num. obs: 60983 / % possible obs: 96.2 % / Redundancy: 1.8 % / Rsym value: 0.042

-
Processing

SoftwareName: REFMAC / Version: 5.3.0036 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I6U

3i6u


Resolution: 3.25→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / SU B: 81.426 / SU ML: 0.579 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.645 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1755 3 %RANDOM
Rwork0.251 ---
obs0.252 56117 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 137.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.34 Å21.73 Å2
2---3.09 Å2-3.45 Å2
3---3.64 Å2
Refinement stepCycle: LAST / Resolution: 3.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24560 0 0 0 24560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02225092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.96633834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44652962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20224.1471196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.937154632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.62315148
X-RAY DIFFRACTIONr_chiral_restr0.0760.23724
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.211364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.217094
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2720
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6190.2247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6260.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4421.2515151
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5742.2524182
X-RAY DIFFRACTIONr_scbond_it2.596211040
X-RAY DIFFRACTIONr_scangle_it4.3573.759652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A951tight positional0.020.03
12B951tight positional0.020.03
13C951tight positional0.030.03
14D951tight positional0.020.03
15E951tight positional0.010.03
16F951tight positional0.010.03
17G951tight positional0.010.03
18H951tight positional0.010.03
21A45tight positional0.030.03
22B45tight positional0.020.03
23C45tight positional0.050.03
24D45tight positional0.030.03
25E45tight positional0.020.03
26F45tight positional0.020.03
27G45tight positional0.020.03
28H45tight positional0.010.03
31A613tight positional0.020.03
32C613tight positional0.020.03
33E613tight positional0.010.03
34G613tight positional0.020.03
41B613tight positional0.020.03
42D613tight positional0.020.03
43F613tight positional0.020.03
44H613tight positional0.010.03
51A510tight positional0.020.03
52B510tight positional0.020.03
53C510tight positional0.030.03
54D510tight positional0.020.03
55E510tight positional0.020.03
56F510tight positional0.020.03
57G510tight positional0.020.03
58H510tight positional0.010.03
61B109tight positional0.020.03
62D109tight positional0.010.03
63F109tight positional0.010.03
64H109tight positional0.010.03
71B77tight positional0.010.03
72D77tight positional0.010.03
73F77tight positional0.010.03
74H77tight positional0.010.03
81A77tight positional0.010.03
82C77tight positional0.010.03
83E77tight positional0.010.03
84G77tight positional0.010.03
91A812tight positional0.020.03
92B812tight positional0.010.03
93C812tight positional0.020.03
94D812tight positional0.010.03
95E812tight positional0.010.03
96F812tight positional0.010.03
97G812tight positional0.010.03
98H812tight positional0.010.03
11A951tight thermal2.646
12B951tight thermal3.116
13C951tight thermal3.766
14D951tight thermal2.366
15E951tight thermal2.396
16F951tight thermal1.756
17G951tight thermal1.776
18H951tight thermal1.816
21A45tight thermal1.546
22B45tight thermal1.756
23C45tight thermal3.266
24D45tight thermal1.686
25E45tight thermal1.466
26F45tight thermal1.796
27G45tight thermal1.556
28H45tight thermal1.926
31A613tight thermal2.36
32C613tight thermal2.386
33E613tight thermal1.776
34G613tight thermal2.146
41B613tight thermal2.636
42D613tight thermal2.726
43F613tight thermal1.896
44H613tight thermal2.196
51A510tight thermal2.946
52B510tight thermal2.416
53C510tight thermal3.596
54D510tight thermal2.366
55E510tight thermal2.896
56F510tight thermal2.526
57G510tight thermal2.526
58H510tight thermal1.696
61B109tight thermal2.976
62D109tight thermal2.266
63F109tight thermal2.416
64H109tight thermal2.086
71B77tight thermal1.476
72D77tight thermal1.636
73F77tight thermal1.276
74H77tight thermal1.56
81A77tight thermal2.346
82C77tight thermal2.096
83E77tight thermal2.236
84G77tight thermal1.26
91A812tight thermal2.656
92B812tight thermal1.866
93C812tight thermal3.86
94D812tight thermal1.696
95E812tight thermal2.246
96F812tight thermal1.886
97G812tight thermal2.326
98H812tight thermal1.846
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 100 -
Rwork0.37 3569 -
obs--77.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
112.27372.3058-1.871414.8407-5.930116.2071-1.09210.4317-0.68760.68851.0821-0.2891-1.0601-1.8860.01-0.38530.2749-0.041-0.48270.0007-0.6622-25.1264-10.856815.5897
29.66121.4360.631412.37110.43497.20580.2657-0.79520.70390.8478-0.0024-0.2093-0.7927-0.1089-0.2633-0.451-0.0191-0.1199-0.6620.0303-0.59910.4045-19.012624.3489
311.03620.67142.935410.61370.61976.3718-0.26080.57761.0029-0.13920.15281.1076-0.215-0.16610.108-0.7641-0.02030.0413-1.00010.0814-0.3869-5.5183-46.607911.7799
47.6261.8042.612320.16972.77199.54760.3123-0.7669-0.27591.1572-0.5097-0.93580.393-0.47010.1974-0.32980.05980.0556-0.07260.0654-0.1026-27.4474-39.900429.2913
519.55149.8367-0.881413.98072.08387.7979-0.4116-0.41540.1611-1.3140.07520.62060.07760.0620.33640.6571-0.0583-0.51-0.66670.3223-0.0229-1.926-35.4486-62.1834
66.0774-0.3079-0.08543.8455-2.02746.9545-0.26060.18230.43640.31660.08440.70280.6059-1.51420.17620.9289-0.3791-0.13220.5202-0.32840.11210.3506-38.6998-33.9671
711.11731.2570.691813.34416.796910.6260.2525-0.7539-0.76090.5825-0.5709-0.72320.0112-0.21020.31840.2903-0.1543-0.14-0.33160.2475-0.02356.4923-69.0285-38.0227
87.87531.02581.963314.9148-0.309410.7368-0.9781-0.1506-0.1831.21090.0560.63-0.4866-1.47530.92210.14290.2590.03910.0962-0.0203-0.4596-17.191-62.0597-52.9382
910.51065.1317-5.86124.2738-2.285610.0374-0.32831.1221-0.6752-0.25810.37190.38140.7149-0.9893-0.0435-0.08210.05070.1819-0.45090.1185-0.13049.0736-12.5657-2.3429
104.52041.3408-1.37467.5445-5.66778.0573-0.2655-0.30320.16291.0890.4813-0.12380.12370.1472-0.2158-0.17130.1135-0.2158-0.70430.0114-0.3709-11.092811.49022.9205
1111.29863.77263.23634.8590.84364.7796-0.1591.281.7355-0.6256-0.014-0.5487-0.7837-0.01810.173-0.30220.12050.1334-0.1760.20180.1641-42.9409-44.39964.4241
126.6693.23723.73719.51487.15847.1930.0862-0.73640.11890.713-0.27810.3540.374-0.19070.1919-0.5477-0.10120.0249-0.66860.1005-0.0622-21.7463-68.63922.9293
1314.35164.4842.20797.16424.06956.0436-0.0550.8661-0.9542-0.5170.1246-0.20191.30210.4893-0.06960.65630.2229-0.3277-0.1561-0.15930.117229.1609-35.4497-38.4328
1414.77642.8102-2.44787.9173-1.59944.82690.8384-0.4384-0.01090.3907-0.3320.76480.3861-0.2253-0.50640.42150.0635-0.2078-0.44680.1035-0.211716.1165-13.4981-58.7491
153.0616-0.5778-2.89968.16477.093110.87580.0959-0.35930.39670.23750.0113-0.7418-0.97860.9632-0.10720.1804-0.05990.09860.2619-0.0183-0.5586-2.379-71.3915-75.7747
165.7325-3.0567-1.749610.71545.82157.49720.015-0.7340.26230.715-0.07780.0597-0.0472-0.6180.06280.33920.0880.1865-0.33240.26080.41725.19-93.4083-53.9454
174.47191.4715-1.434112.19942.1086.9317-0.2712-0.65580.5280.39170.77490.2773-0.35670.3776-0.5036-0.6062-0.046-0.0215-0.3138-0.2806-0.655726.623910.2549-2.891
184.15280.5866-1.22336.32951.84396.456-0.16951.3377-0.5759-0.81020.1741-0.30470.8910.3163-0.0046-0.0411-0.1378-0.132-0.0348-0.0053-0.4188-8.656610.4614-24.5361
193.84860.6024-0.33497.46170.67844.81580.03151.2384-0.2034-0.58060.0371-0.55420.2251-0.5946-0.0686-0.66510.01650.0592-0.1675-0.1463-0.7873-58.1972-69.15277.1354
205.2058-0.81721.05466.413-0.55876.45630.11120.4690.8815-1.0579-0.15660.1003-0.8911-0.60930.0454-0.08120.07120.0208-0.33570.2778-0.2521-32.2244-65.5341-22.6423
219.3819-1.6895-1.76069.77321.36166.1996-0.10030.3007-0.0186-0.8240.6708-0.4526-0.01941.0604-0.5705-0.1495-0.2521-0.0723-0.0607-0.4668-0.743736.8339-9.0444-29.5254
229.8873-1.40091.25594.165-2.13591.87020.82760.9287-0.1453-0.494-0.4984-0.11180.84290.6252-0.32920.72850.5901-0.11180.0804-0.1528-0.510641.8355-18.027-67.6392
232.86072.102-0.77677.6811-0.61925.3399-0.093-0.8777-1.11421.1358-0.05760.69271.2485-1.56430.15070.0311-0.51310.35790.3878-0.0034-0.1398-14.1816-95.5942-86.404
241.54361.622-0.70185.0243-0.54566.20530.01510.52990.3851-0.24330.1794-0.7301-0.53071.143-0.19450.11450.05760.44470.47540.19330.775924.9455-94.7298-73.1323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 207
2X-RAY DIFFRACTION2B92 - 207
3X-RAY DIFFRACTION3C92 - 207
4X-RAY DIFFRACTION4D92 - 207
5X-RAY DIFFRACTION5E92 - 207
6X-RAY DIFFRACTION6F92 - 207
7X-RAY DIFFRACTION7G92 - 207
8X-RAY DIFFRACTION8H92 - 207
9X-RAY DIFFRACTION9A208 - 305
10X-RAY DIFFRACTION10B208 - 305
11X-RAY DIFFRACTION11C208 - 305
12X-RAY DIFFRACTION12D208 - 305
13X-RAY DIFFRACTION13E208 - 305
14X-RAY DIFFRACTION14F208 - 305
15X-RAY DIFFRACTION15G208 - 305
16X-RAY DIFFRACTION16H208 - 305
17X-RAY DIFFRACTION17A306 - 501
18X-RAY DIFFRACTION18B306 - 501
19X-RAY DIFFRACTION19C306 - 501
20X-RAY DIFFRACTION20D306 - 501
21X-RAY DIFFRACTION21E306 - 501
22X-RAY DIFFRACTION22F306 - 501
23X-RAY DIFFRACTION23G306 - 501
24X-RAY DIFFRACTION24H306 - 501

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more