[English] 日本語
Yorodumi
- PDB-5zrf: Crystal structure of human topoisomerase II beta in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zrf
TitleCrystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA topoisomerase 2-beta
  • DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
KeywordsISOMERASE/DNA / Type II topoisomerase / Anti-cancer drug / TopoII cleavage complex / Isomerase-DNA complex / ISOMERASE-DNA-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / forebrain development / DNA topological change / SUMOylation of DNA replication proteins ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / forebrain development / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / axonogenesis / B cell differentiation / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-EVP / DNA / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, S.F. / Wang, Y.R. / Wu, C.C. / Chan, N.L.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
Authors: Chen, S.F. / Huang, N.L. / Lin, J.H. / Wu, C.C. / Wang, Y.R. / Yu, Y.J. / Gilson, M.K. / Chan, N.L.
History
DepositionApr 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 2-beta
B: DNA topoisomerase 2-beta
C: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
D: DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
E: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
F: DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,12914
Polymers196,8066
Non-polymers1,3238
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17030 Å2
ΔGint-99 kcal/mol
Surface area60200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.147, 176.270, 94.331
Angle α, β, γ (deg.)90.00, 111.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / DNA chain / DNA/RNA hybrid , 3 types, 6 molecules ABCEDF

#1: Protein DNA topoisomerase 2-beta / DNA topoisomerase II / beta isozyme


Mass: 91928.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2B / Plasmid: pET51b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02880, EC: 5.99.1.3
#2: DNA chain DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')


Mass: 2436.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA/RNA hybrid DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')


Mass: 4037.988 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 532 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EVP / (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside / Etoposide / VP-16


Mass: 588.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C29H32O13
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Magnesium Acetate, 2-(N-morpholino)ethanesulfonic, 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 99792 / % possible obs: 92.2 % / Redundancy: 2.9 % / CC1/2: 0.93 / Net I/σ(I): 18.4
Reflection shellResolution: 2.3→2.38 Å / CC1/2: 0.738 / Rsym value: 0.473

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QX3

3qx3


Resolution: 2.3→19.869 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1989 1.99 %
Rwork0.1886 --
obs0.1894 99750 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10414 822 90 524 11850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611706
X-RAY DIFFRACTIONf_angle_d0.86316043
X-RAY DIFFRACTIONf_dihedral_angle_d14.016818
X-RAY DIFFRACTIONf_chiral_restr0.0511804
X-RAY DIFFRACTIONf_plane_restr0.0061916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35170.2971310.23876322X-RAY DIFFRACTION83
2.3517-2.41520.26711230.22816447X-RAY DIFFRACTION85
2.4152-2.48610.28651490.22126464X-RAY DIFFRACTION86
2.4861-2.56620.251330.21186603X-RAY DIFFRACTION87
2.5662-2.65770.25441290.20536664X-RAY DIFFRACTION88
2.6577-2.76380.24921440.21126837X-RAY DIFFRACTION90
2.7638-2.88930.26611380.21737007X-RAY DIFFRACTION93
2.8893-3.04110.23311380.21527080X-RAY DIFFRACTION93
3.0411-3.23090.28451450.20457183X-RAY DIFFRACTION95
3.2309-3.47910.23121460.18797263X-RAY DIFFRACTION96
3.4791-3.8270.20021570.17127314X-RAY DIFFRACTION96
3.827-4.37560.18441470.1617427X-RAY DIFFRACTION98
4.3756-5.49340.21971560.16427564X-RAY DIFFRACTION99
5.4934-19.86960.20061530.18957586X-RAY DIFFRACTION99
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)
10.01110.0250.03520.01680.01150.03480.19560.15180.0913-0.64690.0115-0.041-0.25740.23430.04150.65850.19350.11170.8818-0.10240.433349.190386.343639.9346
20.02280.1074-0.20820.2154-0.17340.15850.13480.89470.1388-0.1069-0.1136-0.2031-0.0983-0.02620.00030.39790.12780.09290.7214-0.01550.481954.254489.196646.8487
30.11520.1530.0080.16070.0693-0.00160.12850.70030.0431-0.3708-0.17150.0839-0.07790.2951-0.02490.50970.15390.15390.78290.05910.460955.551189.893144.901
40.07730.0076-0.01690.0090.03190.05790.0839-0.0382-0.2722-0.0913-0.1316-0.46110.2011-0.1131-0.00010.43670.03630.05020.41580.01740.462937.501282.906658.1861
50.10150.1286-0.11590.0419-0.26380.1825-0.36630.2846-0.4307-0.4157-0.12230.17040.2789-0.0135-0.01020.53870.13150.08520.4856-0.13340.637543.789775.283351.2914
60.1899-0.08410.11660.0131-0.07930.19250.0915-0.01960.0943-0.27690.1903-0.17340.00340.26690.00060.32390.13560.06630.5401-0.03890.366253.247484.872352.9036
70.34680.0695-0.10940.029-0.11720.29060.0287-0.1118-0.1047-0.25780.04880.0959-0.010.29330.00020.31770.103-0.04680.456-0.00720.44244.81684.90261.6361
80.0150.05230.02490.08660.03570.0150.1186-0.3621-0.4161-0.4812-0.14170.23350.0445-0.05190.00240.50740.10280.01310.5998-0.0020.722353.692674.32159.8331
90.0170.0018-0.03270.02640.0148-0.00540.34170.29520.2460.0152-0.0241-0.17110.0331-0.055100.46090.19110.00840.5867-0.09480.633755.616589.281658.0865
100.0097-0.0185-0.00430.0109-0.00320.0040.2814-0.1321-0.04620.21-0.1146-0.3326-0.01370.18670.00010.6273-0.15950.12270.8489-0.09170.930259.4114101.596850.6498
110.2931-0.06040.23850.30660.33780.65220.52370.5322-0.23490.06670.4277-0.48140.09451.27310.4701-0.23630.49130.26120.7689-0.07810.576959.799488.543261.2956
120.01320.0026-0.06710.1767-0.10020.2226-0.0976-0.2081-0.3847-0.3662-0.20710.08360.38540.5253-0.14860.38510.25660.01940.58380.12430.520646.52479.504671.1218
130.978-0.21130.00810.0392-0.0660.2284-0.214-0.5064-0.61880.21050.4497-0.20620.26550.3533-0.07370.43330.1327-0.07470.62250.04640.335440.721989.700179.7869
140.1677-0.0756-0.19010.31020.33740.5352-0.0404-0.06440.02130.11280.1668-0.0221-0.08230.18790.00260.26630.018-0.00680.3819-0.01020.30434.6243104.229167.5638
150.30570.4236-0.01890.40060.65420.0685-0.08920.1529-0.0417-0.16540.1040.0775-0.0413-0.00200.30310.0585-0.03540.32250.02280.265619.4118105.580759.3237
160.288-0.3775-0.41130.24280.22850.72930.0621-0.10490.0189-0.04270.0001-0.088-0.00810.056100.32630.00950.03770.3199-0.00750.322425.7889108.557175.5856
170.34780.75960.65311.51971.00330.77040.0595-0.09050.03720.1921-0.19180.26730.2029-0.1083-00.29670.03090.03320.3469-0.04030.38012.652888.139666.5597
18-0.15570.1-0.03980.96080.61861.09340.0288-0.0378-0.0480.30110.071-0.0294-0.0848-0.01150.06010.31330.00290.0070.32710.01060.223124.9957118.372485.598
190.62960.03520.0470.3456-0.37930.33530.0792-0.1897-0.23160.8447-0.2459-0.1235-0.60730.332-0.01360.6635-0.0741-0.01520.4180.02630.397937.177147.957983.7456
20-0.14520.206-0.21530.5264-0.22430.5110.1613-0.00060.07560.2648-0.03790.2806-0.2725-0.0685-0.00260.54840.0350.09350.36390.06090.322522.886143.708181.9663
210.2938-0.1412-0.17910.5647-0.1010.14730.0151-0.01240.04640.0237-0.03750.0977-0.3781-0.1583-0.00020.34570.06990.02950.3439-0.0340.34387.9196115.325776.4301
22-0.00240.0110.00770.0347-0.03870.02340.00840.4782-0.3220.19130.3428-0.26430.21510.35880.00040.4620.0696-0.00370.41470.04240.704713.966486.893834.5088
230.1917-0.08820.04670.029-0.03060.12960.0167-0.2673-0.119-0.0630.10790.4229-0.02270.07960.00480.3388-0.0894-0.07390.33130.07070.68215.026492.210430.6391
240.04380.01040.00490.04660.05050.0980.1394-0.2793-0.31460.51140.10970.08120.1993-0.02930.00490.4898-0.15150.0440.57190.10230.68446.836898.075341.2349
250.0051-0.0262-0.00980.04390.0139-0.02640.1294-0.3503-0.26820.049-0.01510.579-0.1239-0.02830.00010.3655-0.02530.07340.40520.03550.64257.257394.723333.8762
260.0779-0.0025-0.00260.05670.0246-0.00220.08530.04440.0331-0.391-0.1186-0.08190.17380.0131-0.00030.3135-0.0346-0.01670.307-0.02440.36623.392101.631421.7983
270.1129-0.05710.01210.1008-0.14140.14490.0809-0.5239-0.342-0.3322-0.00820.07860.0570.388800.46310.0326-0.05730.3482-0.0170.460922.033792.221723.518
280.24080.0076-0.07060.03550.17760.68220.1553-0.14330.0941-0.60920.17620.55661.04940.08320.01360.6174-0.1703-0.20920.2938-0.04120.49269.318588.948314.0523
290.6511-0.1926-0.05150.28710.07970.94950.0793-0.00440.0673-0.34230.05080.5129-0.012-0.11010.14140.3177-0.0376-0.11410.2674-0.00690.464511.8789101.630624.472
300.0114-0.01490.0110.02160.02590.00660.1920.25470.0424-0.19760.093-0.22020.2422-0.2192-00.4977-0.0003-0.27140.4105-0.03910.54237.422697.478714.4833
310.0295-0.10480.0730.519-0.63930.77890.3037-0.5841-0.2003-0.07860.55810.82040.01720.1050.15920.2530.0346-0.00410.4605-0.02380.72135.3118105.640528.5826
320.0734-0.00520.08050.4532-0.26710.268-0.0576-0.8681-0.08050.13830.27030.84170.1833-0.12730.03270.3744-0.01350.26820.6751-0.07540.87260.4443106.476239.844
330.10970.04630.16470.34560.02220.667-0.16710.20440.0908-0.30780.05710.5786-0.1714-0.0665-0.06140.3046-0.0267-0.21750.2978-0.01160.5369.1953108.638915.3595
340.29120.0839-0.07330.0921-0.0790.0592-0.08820.38410.2256-0.4890.12370.3478-0.30710.09240.01050.43250.0462-0.07960.36110.09010.486318.8914124.557916.0119
350.22440.47880.09121.10270.25250.5110.0115-0.03260.04240.0411-0.01710.2455-0.17810.03790.00410.2493-0.01450.0090.3072-0.00650.330625.644121.01534.5984
360.52060.2999-0.4880.55240.1990.32770.0472-0.0614-0.11620.0448-0.02190.10050.02330.062200.3042-0.0633-0.02870.32160.01070.280540.6292119.039440.6918
370.1165-0.2253-0.10650.34690.17560.11420.09730.1326-0.14970.2678-0.13880.182-0.2108-0.09170.00120.3667-0.02830.0560.3441-0.01480.368527.5015133.298338.1473
380.0735-0.336-0.14110.4528-0.00150.58050.07360.0350.0828-0.2135-0.0027-0.1325-0.18960.080100.3053-0.04220.04090.3015-0.01420.27248.2974127.3922.9738
390.2316-0.28290.07670.2874-0.26650.71580.13110.0747-0.20890.1664-0.0472-0.27110.1078-0.0630.03640.235-0.0383-0.04460.3405-0.05850.538658.9534103.181624.4612
400.9076-0.23780.24770.42030.08850.56570.0957-0.5387-0.65250.13720.3722-0.2840.42510.13280.11630.5066-0.0958-0.03760.3871-0.1440.779762.476194.81323.9088
410.01060.01980.01780.0520.02340.0485-0.7911-0.1179-0.31180.65460.5097-0.2417-0.30220.36770.00060.47790.0858-0.07130.5136-0.00060.410260.4126106.887435.013
420.12130.11550.05690.2844-0.03080.0250.18270.4166-0.48260.0577-0.2978-0.2403-0.4046-0.194-0.0080.25540.03540.0710.4716-0.07980.525568.396799.229218.085
430.0023-0.01890.00950.0958-0.03250.0122-0.14430.32630.0895-0.4174-0.2531-0.0536-0.1421-0.1239-0.00320.449-0.0188-0.00680.5164-0.1060.466661.7455106.131514.0303
440.1210.0209-0.16390.0052-0.02620.16250.39750.2570.1212-0.5588-0.15520.036-0.17710.2814-0.00090.4485-0.0129-0.00810.4303-0.03270.348950.3428112.989516.5593
450.05030.02950.12640.04850.03960.13920.06880.38350.7252-0.0465-0.12330.028-0.2559-0.0725-00.4322-0.0017-0.07430.3870.02240.367932.5964130.384119.9688
46-0.0311-0.2011-0.03310.4317-0.00040.2978-0.00370.10090.0121-0.0364-0.06470.0369-0.2861-0.045-0.00260.3917-0.05160.02640.30060.0260.32636.0991150.365143.3043
470.04060.06670.12940.02480.09470.11370.1039-0.32690.42480.75860.13930.5397-0.908-0.6261-0.00020.9050.13190.11030.47280.05550.559121.2792162.95768.8056
480.06750.0678-0.05510.0369-0.03490.02480.56040.2409-0.05420.2349-0.3167-0.5157-0.40760.4358-0.00040.6001-0.02770.00490.38560.06280.482625.2413162.024658.6662
490.0078-0.0026-0.01120.0032-0.00020.0091-0.05740.3434-0.1551-0.3009-0.1877-0.1683-0.0022-0.157700.52650.0046-0.00330.4455-0.02050.442725.4255151.547747.4456
500.0444-0.0769-0.08670.0979-0.10170.11330.2170.3395-0.11220.3694-0.0628-0.0579-0.00240.1631-0.00010.5643-0.02350.08870.38210.04590.369829.0088154.043766.0136
51-0.09560.2701-0.1268-0.1270.2670.2050.02440.0012-0.22150.0679-0.0692-0.0522-0.62051.08-0.00060.5278-0.05580.00610.39830.06730.362542.9758156.599354.2196
520.37240.215-0.14090.23220.14780.2264-0.0306-0.2676-0.00440.25740.1666-0.0273-0.16650.117600.3588-0.0492-0.02070.3516-0.04140.36452.4074134.957739.0578
530.2354-0.1343-0.18080.0928-0.00220.1756-0.03380.1051-0.2912-0.19360.05440.05070.16260.0217-0.00010.39590.0162-0.03230.30430.01160.367126.31490.52861.8902
540.1686-0.268-0.1172-0.1233-0.1988-0.14960.2031-0.1020.0104-0.2484-0.11910.05280.19690.5518-0.00010.3930.0187-0.02020.43680.0070.296832.3993105.436827.3457
550.17920.02940.01420.2677-0.34050.2422-0.30180.0873-0.23040.21210.1231-0.07780.64930.28070.00010.40930.01620.01840.4405-0.02120.347634.5058108.751126.6758
560.42620.27820.0896-0.2544-0.2332-0.00260.0298-0.0003-0.068-0.29730.26570.1260.6635-0.0020.00120.48560.033-0.02890.40210.08880.422328.397789.159358.6743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 452 through 461 )
2X-RAY DIFFRACTION2chain 'A' and (resid 462 through 489 )
3X-RAY DIFFRACTION3chain 'A' and (resid 490 through 502 )
4X-RAY DIFFRACTION4chain 'A' and (resid 503 through 513 )
5X-RAY DIFFRACTION5chain 'A' and (resid 514 through 542 )
6X-RAY DIFFRACTION6chain 'A' and (resid 543 through 559 )
7X-RAY DIFFRACTION7chain 'A' and (resid 560 through 576 )
8X-RAY DIFFRACTION8chain 'A' and (resid 577 through 583 )
9X-RAY DIFFRACTION9chain 'A' and (resid 584 through 591 )
10X-RAY DIFFRACTION10chain 'A' and (resid 638 through 645 )
11X-RAY DIFFRACTION11chain 'A' and (resid 646 through 658 )
12X-RAY DIFFRACTION12chain 'A' and (resid 659 through 670 )
13X-RAY DIFFRACTION13chain 'A' and (resid 671 through 694 )
14X-RAY DIFFRACTION14chain 'A' and (resid 707 through 771 )
15X-RAY DIFFRACTION15chain 'A' and (resid 772 through 828 )
16X-RAY DIFFRACTION16chain 'A' and (resid 829 through 884 )
17X-RAY DIFFRACTION17chain 'A' and (resid 885 through 1012 )
18X-RAY DIFFRACTION18chain 'A' and (resid 1013 through 1075 )
19X-RAY DIFFRACTION19chain 'A' and (resid 1076 through 1111 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1135 through 1175 )
21X-RAY DIFFRACTION21chain 'A' and (resid 1176 through 1201 )
22X-RAY DIFFRACTION22chain 'B' and (resid 449 through 458 )
23X-RAY DIFFRACTION23chain 'B' and (resid 459 through 478 )
24X-RAY DIFFRACTION24chain 'B' and (resid 479 through 494 )
25X-RAY DIFFRACTION25chain 'B' and (resid 495 through 502 )
26X-RAY DIFFRACTION26chain 'B' and (resid 503 through 513 )
27X-RAY DIFFRACTION27chain 'B' and (resid 514 through 530 )
28X-RAY DIFFRACTION28chain 'B' and (resid 531 through 542 )
29X-RAY DIFFRACTION29chain 'B' and (resid 543 through 576 )
30X-RAY DIFFRACTION30chain 'B' and (resid 577 through 583 )
31X-RAY DIFFRACTION31chain 'B' and (resid 584 through 592 )
32X-RAY DIFFRACTION32chain 'B' and (resid 637 through 650 )
33X-RAY DIFFRACTION33chain 'B' and (resid 651 through 670 )
34X-RAY DIFFRACTION34chain 'B' and (resid 671 through 695 )
35X-RAY DIFFRACTION35chain 'B' and (resid 706 through 771 )
36X-RAY DIFFRACTION36chain 'B' and (resid 772 through 841 )
37X-RAY DIFFRACTION37chain 'B' and (resid 842 through 861 )
38X-RAY DIFFRACTION38chain 'B' and (resid 862 through 926 )
39X-RAY DIFFRACTION39chain 'B' and (resid 927 through 962 )
40X-RAY DIFFRACTION40chain 'B' and (resid 967 through 975 )
41X-RAY DIFFRACTION41chain 'B' and (resid 976 through 983 )
42X-RAY DIFFRACTION42chain 'B' and (resid 984 through 998 )
43X-RAY DIFFRACTION43chain 'B' and (resid 999 through 1004 )
44X-RAY DIFFRACTION44chain 'B' and (resid 1005 through 1015 )
45X-RAY DIFFRACTION45chain 'B' and (resid 1016 through 1030 )
46X-RAY DIFFRACTION46chain 'B' and (resid 1031 through 1076 )
47X-RAY DIFFRACTION47chain 'B' and (resid 1077 through 1095 )
48X-RAY DIFFRACTION48chain 'B' and (resid 1096 through 1101 )
49X-RAY DIFFRACTION49chain 'B' and (resid 1102 through 1110 )
50X-RAY DIFFRACTION50chain 'B' and (resid 1135 through 1150 )
51X-RAY DIFFRACTION51chain 'B' and (resid 1151 through 1175 )
52X-RAY DIFFRACTION52chain 'B' and (resid 1176 through 1201 )
53X-RAY DIFFRACTION53chain 'C' and (resid 1 through 8 )
54X-RAY DIFFRACTION54chain 'D' and (resid 10 through 19 )
55X-RAY DIFFRACTION55chain 'E' and (resid 1 through 8 )
56X-RAY DIFFRACTION56chain 'F' and (resid 10 through 19 )

+
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