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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zen
TitleCrystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
  • DNA topoisomerase 2-beta
KeywordsISOMERASE/DNA / Type II topoisomerase / cleavage complex / DNA-gate / ISOMERASE-DNA 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 negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / 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 negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / B cell differentiation / axonogenesis / cellular response to hydrogen peroxide / neuron migration / 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 / 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
: / DNA / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsChen, S.F. / Wang, Y.R. / 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
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 2-beta
B: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2075
Polymers97,0973
Non-polymers1102
Water34219
1
A: DNA topoisomerase 2-beta
B: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
hetero molecules

A: DNA topoisomerase 2-beta
B: DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,41310
Polymers194,1946
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area10680 Å2
ΔGint-93 kcal/mol
Surface area64330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.760, 95.760, 231.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 91928.367 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')


Mass: 2731.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.95 %
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: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 32586 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.983 / Net I/σ(I): 33.3
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.483 / CC1/2: 0.913

-
Processing

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

3qx3


Resolution: 2.75→19.97 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.08
RfactorNum. reflection% reflection
Rfree0.266 2006 6.17 %
Rwork0.221 --
obs0.224 32531 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 349 2 19 5731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075905
X-RAY DIFFRACTIONf_angle_d0.7828095
X-RAY DIFFRACTIONf_dihedral_angle_d12.9693454
X-RAY DIFFRACTIONf_chiral_restr0.05923
X-RAY DIFFRACTIONf_plane_restr0.006983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7507-2.81930.28851390.28542136X-RAY DIFFRACTION99
2.8193-2.89530.36441360.28472120X-RAY DIFFRACTION100
2.8953-2.98020.36011370.28222173X-RAY DIFFRACTION100
2.9802-3.07610.32531430.2952137X-RAY DIFFRACTION100
3.0761-3.18560.35171400.27912153X-RAY DIFFRACTION100
3.1856-3.31260.29361420.26862172X-RAY DIFFRACTION100
3.3126-3.46260.3391410.25282154X-RAY DIFFRACTION100
3.4626-3.64410.26851450.23142158X-RAY DIFFRACTION100
3.6441-3.87090.24741420.21482171X-RAY DIFFRACTION100
3.8709-4.16720.27121450.19832206X-RAY DIFFRACTION100
4.1672-4.5820.20911430.18942179X-RAY DIFFRACTION100
4.582-5.23460.21641430.19052210X-RAY DIFFRACTION100
5.2346-6.55610.28391490.22982234X-RAY DIFFRACTION100
6.5561-19.97090.24721610.19472322X-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)
12.5503-1.047-1.18093.75050.72234.2505-0.16880.0012-0.3985-0.0608-0.08180.31210.57820.010.3360.4683-0.0077-0.02940.61990.01670.358638.8486-32.8734-58.0484
29.0778-1.7817-0.14936.7488-4.54067.808-0.43990.2333-1.14620.82480.1203-0.03270.81971.7280.2150.71940.23120.02650.7580.08530.502650.9125-32.4082-37.8601
32.6443-0.48920.23633.72-0.06152.8877-0.8882-0.3746-0.01670.36690.69620.06951.83151.00420.55560.75450.18760.05770.74050.14850.474550.3643-36.5619-49.9774
41.2878-0.3132-0.63384.08092.83353.58120.11430.09150.0558-0.1983-0.1215-0.3330.40180.10940.11510.47920.01350.04990.62870.08020.400247.5306-26.619-52.8633
52.02170.42210.79473.33851.48720.8344-0.1211-0.6412-0.2445-0.9642-0.0050.165-0.48520.53670.6160.64880.0090.11641.01690.01110.527157.8832-27.7039-54.6761
65.5535-5.07123.86134.611-3.70883.78180.45391.3241-0.4155-0.6049-1.22410.112-0.1291-0.05840.61160.61770.11260.03850.82610.08740.382445.1047-22.1506-58.9836
71.6098-1.486-2.84074.92661.72545.24440.1606-1.2407-0.7892-1.02120.00650.685-0.7496-1.28780.0770.9009-0.1101-0.1221.266-0.11980.763527.4284-20.0627-56.6337
87.8095-2.5018-3.34263.5243.33453.39520.9519-0.67891.0047-0.017-1.49670.53390.58950.27060.64161.3418-0.1318-0.23442.1065-0.08930.979130.5966-21.31-65.8607
91.5377-0.24761.07493.5287-0.75793.00520.03921.54090.4964-0.1362-0.35790.0009-0.1440.80440.04070.80170.06330.16791.17960.11410.685548.0995-18.4851-62.219
100.2379-1.08920.12057.82062.64073.6147-0.49321.1571-0.65390.2131-0.1099-1.00910.78891.1720.73030.5367-0.03980.15071.16280.14160.504356.7234-16.7883-45.5773
118.3256-4.26040.61786.2472.40111.7090.46260.28421.4258-1.901-0.5515-0.89180.03280.46130.43470.6856-0.1364-0.01430.82360.1320.731849.8399-3.7015-40.7708
120.1283-0.75250.41781.79010.57251.85420.09870.42870.2189-0.3585-0.2420.0284-0.217-0.13050.19890.4193-0.07960.00120.71590.08710.440543.1632-9.9083-43.0383
131.2292-0.16051.3573.28230.44114.22170.10690.0255-0.1234-0.325-0.05240.30870.1539-0.2560.01050.2986-0.116-0.0350.48050.00570.43921.397-13.9533-29.8168
144.1595-2.84151.56568.84981.65953.23090.56090.0658-0.8139-0.0449-0.53350.86810.5839-0.26980.0260.4714-0.20580.01530.51370.06080.475820.9697-22.2745-23.8829
152.3328-0.54570.73570.48370.43581.4832-0.57780.3891-0.02150.0569-0.1903-0.7363-0.67380.44790.76430.32670.0504-0.06320.4972-0.0360.550620.22632.6894-25.326
163.34780.34650.35063.86632.57932.1707-0.26181.16830.4573-0.6296-0.28860.3423-0.92310.20140.54950.505-0.1207-0.1690.71010.13670.692425.69041.3377-36.0559
171.9206-1.6499-0.18371.9661-0.1233.0025-0.14530.09030.04020.3284-0.1263-0.1127-0.03930.24650.24920.375-0.1207-0.03550.55380.00880.520835.1019-3.825-17.4026
180.6785-1.5121-0.21237.5207-1.2221.68910.1661-0.31850.17852.1506-0.3326-0.2605-0.3790.35580.12430.5845-0.1484-0.15380.53160.0150.493737.7691-7.6449-7.9488
194.49522.9299-3.58653.686-4.23868.4589-0.14150.22940.08090.3805-0.0603-0.3045-0.25680.10580.20270.4249-0.1023-0.06130.53250.00460.409340.3592-23.8524-0.7972
203.5617-2.60520.87258.719-1.46064.9072-0.02970.6204-0.193-0.7724-0.3821-0.26510.78330.16830.26660.5274-0.11390.07750.42280.04250.357436.6516-31.2944-9.8927
211.465-1.40671.13682.74470.26049.1878-0.41330.87890.1298-0.3994-0.10420.09281.43620.84360.21230.72610.0259-0.03460.7290.03810.569639.8937-40.6826-5.4017
224.5262-2.68111.42254.4494-1.84062.9104-0.0667-0.1658-0.01610.29770.01560.07040.0020.1270.02320.6047-0.1216-0.01060.46690.01760.412239.1645-32.56120.2048
232.15810.2607-0.53142.1875-0.38650.275-0.08470.2890.60870.4608-0.3159-0.9439-0.47490.41130.38290.4136-0.134-0.04690.62710.07010.520443.3774-7.3324-20.5058
242.8818-0.08481.393-0.1655-1.04350.8212-0.254-1.11490.7607-0.36570.27520.4016-0.5-0.36990.18870.86750.1248-0.37110.3952-0.13111.214710.908319.7955-31.7189
252.5468-3.2928-0.59465.5472-1.91926.0418-0.2767-0.81290.769-1.1196-0.11271.6240.430.45880.4150.87770.1143-0.64430.545-0.04121.538210.812122.1948-38.7966
262.21371.60651.10445.0205-0.65674.7734-0.6912-0.18910.0470.1394-0.9840.7744-1.4487-0.99161.13191.1360.301-0.75210.2493-0.04041.7379-4.109719.6537-38.5662
273.8912-0.83783.18881.2009-0.35642.8534-0.7952-0.49070.81750.19280.4020.1132-0.4742-0.65140.47480.51820.0315-0.08490.6052-0.11530.827512.92119.0747-16.404
284.3278-1.43143.80581.3988-2.40144.74420.22550.24241.0889-0.60790.07771.1451-0.808-0.4335-0.44511.00840.3666-0.10941.82850.00590.81130.7564-9.6161-59.336
290.927-0.99380.03563.565-1.17160.5276-0.0192-0.16980.8107-0.9421.1691-1.07110.3235-0.1847-0.47341.46120.1239-0.12730.99860.24611.401434.7882-8.4632-61.4067
301.0946-0.72182.04680.5275-1.29773.8383-0.923-0.44980.72450.3047-0.5760.4516-1.1282-0.66391.06961.8710.3097-0.22161.4668-0.12261.633734.1016-0.7527-58.0516
314.53182.4265-2.41493.55611.7415.3721.10250.0079-1.14770.3362-0.0998-1.01-0.35920.1123-0.34761.13420.1338-0.24881.81620.2851.186226.5439-10.3473-56.1441
327.7469-5.0261-0.24284.3676-2.52027.072-0.01371.5510.62080.727-0.37420.4772-1.21340.16640.79671.1950.2068-0.16120.9461-0.06881.052343.3655-4.9671-56.1422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 452 THROUGH 508 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 509 THROUGH 520 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 521 THROUGH 538 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 540 THROUGH 576 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 577 THROUGH 583 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 584 THROUGH 591 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 632 THROUGH 636 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 637 THROUGH 645 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 646 THROUGH 658 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 659 THROUGH 670 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 671 THROUGH 696 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 707 THROUGH 739 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 740 THROUGH 808 )
14X-RAY DIFFRACTION14CHAIN 'A' AND (RESID 809 THROUGH 828 )
15X-RAY DIFFRACTION15CHAIN 'A' AND (RESID 829 THROUGH 841 )
16X-RAY DIFFRACTION16CHAIN 'A' AND (RESID 842 THROUGH 861 )
17X-RAY DIFFRACTION17CHAIN 'A' AND (RESID 862 THROUGH 897 )
18X-RAY DIFFRACTION18CHAIN 'A' AND (RESID 898 THROUGH 919 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID 920 THROUGH 936 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 937 THROUGH 961 )
21X-RAY DIFFRACTION21CHAIN 'A' AND (RESID 962 THROUGH 976 )
22X-RAY DIFFRACTION22CHAIN 'A' AND (RESID 978 THROUGH 1004 )
23X-RAY DIFFRACTION23CHAIN 'A' AND (RESID 1005 THROUGH 1032 )
24X-RAY DIFFRACTION24CHAIN 'A' AND (RESID 1033 THROUGH 1095 )
25X-RAY DIFFRACTION25CHAIN 'A' AND (RESID 1096 THROUGH 1111 )
26X-RAY DIFFRACTION26CHAIN 'A' AND (RESID 1135 THROUGH 1150 )
27X-RAY DIFFRACTION27CHAIN 'A' AND (RESID 1151 THROUGH 1201 )
28X-RAY DIFFRACTION28CHAIN 'A' AND (RESID 592 THROUGH 596 )
29X-RAY DIFFRACTION29CHAIN 'A' AND (RESID 603 THROUGH 607 )
30X-RAY DIFFRACTION30CHAIN 'A' AND (RESID 608 THROUGH 615 )
31X-RAY DIFFRACTION31CHAIN 'A' AND (RESID 625 THROUGH 631 )
32X-RAY DIFFRACTION32CHAIN 'A' AND (RESID 697 THROUGH 702 )

+
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