[English] 日本語
Yorodumi
- PDB-7s6m: Human PARP1 deltaV687-E688 bound to a DNA double strand break. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s6m
TitleHuman PARP1 deltaV687-E688 bound to a DNA double strand break.
Components
  • DNA (5'-D(*CP*GP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*CP*G)-3')
  • Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
  • Poly [ADP-ribose] polymerase 1
KeywordsDNA BINDING PROTEIN/DNA / PARP / ADP-ribose transferase / DNA break detection / zinc finger / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / signal transduction involved in regulation of gene expression / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / mitochondrial DNA repair / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / NAD+-protein-glutamate ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / cellular response to zinc ion / NAD+-protein mono-ADP-ribosyltransferase activity / R-SMAD binding / nuclear replication fork / protein autoprocessing / site of DNA damage / decidualization / NAD+ poly-ADP-ribosyltransferase activity / negative regulation of transcription elongation by RNA polymerase II / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / telomere maintenance / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / enzyme activator activity / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to nerve growth factor stimulus / DNA Damage Recognition in GG-NER / protein-DNA complex / protein modification process / Dual Incision in GG-NER / positive regulation of protein localization to nucleus / Formation of Incision Complex in GG-NER / histone deacetylase binding / cellular response to insulin stimulus / NAD binding / cellular response to amyloid-beta / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription by RNA polymerase II / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRouleau-Turcotte, E. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT173370 Canada
CitationJournal: Mol.Cell / Year: 2022
Title: Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery.
Authors: Rouleau-Turcotte, E. / Krastev, D.B. / Pettitt, S.J. / Lord, C.J. / Pascal, J.M.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 31, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: DNA (5'-D(*CP*GP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*CP*G)-3')
N: DNA (5'-D(*CP*GP*AP*CP*G)-3')
D: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
M: DNA (5'-D(*CP*GP*TP*CP*G)-3')
A: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
C: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,79515
Polymers182,3488
Non-polymers4487
Water1086
1
O: DNA (5'-D(*CP*GP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*CP*G)-3')
D: Poly [ADP-ribose] polymerase 1
C: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3677
Polymers91,1744
Non-polymers1933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: DNA (5'-D(*CP*GP*AP*CP*G)-3')
B: Poly [ADP-ribose] polymerase 1
M: DNA (5'-D(*CP*GP*TP*CP*G)-3')
A: Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4298
Polymers91,1744
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.705, 112.074, 116.482
Angle α, β, γ (deg.)90.000, 114.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 400 or resid 500))
21(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))
12(chain B and (resid 531 through 646 or resid 663...
22(chain D and (resid 531 through 646 or resid 663...
13chain M
23chain P
14chain N
24chain O

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 400 or resid 500))A0
211(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))C6 - 91
221(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))C227 - 400
231(chain C and (resid 6 through 91 or resid 227 through 400 or resid 500))C500
112(chain B and (resid 531 through 646 or resid 663...B531 - 646
122(chain B and (resid 531 through 646 or resid 663...B663
132(chain B and (resid 531 through 646 or resid 663...B665 - 689
142(chain B and (resid 531 through 646 or resid 663...B691 - 1020
152(chain B and (resid 531 through 646 or resid 663...B1101
212(chain D and (resid 531 through 646 or resid 663...D531 - 646
222(chain D and (resid 531 through 646 or resid 663...D663
232(chain D and (resid 531 through 646 or resid 663...D665 - 689
242(chain D and (resid 531 through 646 or resid 663...D691 - 780
252(chain D and (resid 531 through 646 or resid 663...D787 - 1020
262(chain D and (resid 531 through 646 or resid 663...D1101
113chain MM22 - 26
213chain PP22 - 26
114chain NN1 - 5
214chain OO1 - 5

NCS ensembles :
ID
1
2
3
4

-
Components

-
DNA chain , 2 types, 4 molecules ONPM

#1: DNA chain DNA (5'-D(*CP*GP*AP*CP*G)-3')


Mass: 1505.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*G)-3')


Mass: 1496.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein , 2 types, 4 molecules DBAC

#3: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 56909.910 Da / Num. of mol.: 2 / Mutation: deltaV687-E688
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#4: Protein Fusion of human PARP1 zinc fingers 1 and 3 (Zn1, Zn3) / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 31262.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

-
Non-polymers , 3 types, 13 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.2→39.15 Å / Num. obs: 42258 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Rrim(I) all: 0.083 / Net I/σ(I): 12.6 / Num. measured all: 175073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.2-3.324.31.7291879544030.3150.9471.9790.999.5
11.97-39.153.90.02631818260.9980.0140.02948.596.5

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQY

4dqy


Resolution: 3.2→39.15 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1990 4.71 %
Rwork0.2064 40221 -
obs0.2081 42211 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 321.98 Å2 / Biso mean: 142.9915 Å2 / Biso min: 63.76 Å2
Refinement stepCycle: final / Resolution: 3.2→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10925 398 31 6 11360
Biso mean--121.27 78.62 -
Num. residues----1399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1723X-RAY DIFFRACTIONPOSITIONAL0.013
12C1723X-RAY DIFFRACTIONPOSITIONAL0.013
21B3696X-RAY DIFFRACTIONPOSITIONAL0.052
22D3696X-RAY DIFFRACTIONPOSITIONAL0.052
31M99X-RAY DIFFRACTIONPOSITIONAL0.004
32P99X-RAY DIFFRACTIONPOSITIONAL0.004
41N100X-RAY DIFFRACTIONPOSITIONAL0.006
42O100X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.280.42031560.38792805296199
3.28-3.370.40371290.34752862299199
3.37-3.470.33921400.314828582998100
3.47-3.580.32341260.28282881300799
3.58-3.710.30591330.264228532986100
3.71-3.860.33251540.25228693023100
3.86-4.030.30111680.229928463014100
4.03-4.240.23661350.191428893024100
4.24-4.510.22341190.17728883007100
4.51-4.860.20271300.16928913021100
4.86-5.340.23591490.168328823031100
5.34-6.110.26881420.198128933035100
6.12-7.690.23811290.20692905303499
7.69-39.150.18371800.18372899307999
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)
10.0694-0.01930.05940.0165-0.01090.0477-0.5421-0.5921.1796-0.95050.26470.78080.12260.2471-0.00281.2181-0.0246-0.04261.20980.0591.3026-2.936535.715366.7593
20.0242-0.0064-0.01720.02150.05680.14180.5635-0.29850.2125-0.88-0.7994-0.41250.48560.96830.00011.58340.0774-0.12350.93570.17681.5465-6.003930.964661.0813
30.05860.03550.06440.02060.03670.06341.0068-0.051-0.0962-0.29680.24281.15730.38570.9330.00171.07440.0045-0.11781.08080.05141.225-4.84011.166971.4259
41.8709-0.3371-0.99231.06720.17620.1146-0.0011-0.05010.17650.2170.1383-0.26620.0867-0.0489-01.3422-0.0819-0.06591.24030.01751.05541.451334.594656.9827
5-0.17240.26331.09160.5750.15942.75070.03230.05460.05850.1620.0599-0.19380.39060.0730.00011.10060.05180.14211.2390.06651.19916.29942.7529111.8017
60.012-0.01780.01560.0248-0.03290.04420.9567-0.6363-0.25040.2981-0.40690.81730.01930.3973-0.00091.249-0.0560.11710.88430.06561.5236-11.17755.830372.8166
71.15150.4021-0.72361.0044-0.72021.18620.1651-0.09920.11910.3548-0.14470.6258-0.352-0.3765-0.00020.97640.0210.06051.2001-0.07411.5292-24.487415.153580.0353
81.3825-0.24680.41251.1637-0.74271.28440.1080.29640.0333-0.7501-0.20580.04380.03210.1045-0.00021.40750.0922-0.26931.1455-0.00211.0994-8.947821.534745.8347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'O' and resid 1 through 5)O1 - 5
2X-RAY DIFFRACTION2(chain 'P' and resid 22 through 26)P22 - 26
3X-RAY DIFFRACTION3(chain 'N' and resid 1 through 5)N1 - 5
4X-RAY DIFFRACTION4(chain 'D' and resid 531 through 1020)D531 - 1020
5X-RAY DIFFRACTION5(chain 'B' and resid 531 through 1020)B531 - 1020
6X-RAY DIFFRACTION6(chain 'M' and resid 22 through 26)M22 - 26
7X-RAY DIFFRACTION7(chain 'A' and resid 6 through 359)A6 - 359
8X-RAY DIFFRACTION8(chain 'C' and resid 6 through 359)C6 - 359

+
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