[English] 日本語
Yorodumi
- PDB-6zx9: Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zx9
TitleCrystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396)
Components
  • DDB1- and CUL4-associated factor 1
  • DNA damage-binding protein 1
  • Vpr protein fused to T4 lysozyme
KeywordsVIRAL PROTEIN / viral protein Vpr / viral hijacking of human ubiquitin ligase CRL4 / DDB1 / DCAF1
Function / homology
Function and homology information


histone H2AT120 kinase activity / cell competition in a multicellular organism / virion component => GO:0044423 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont ...histone H2AT120 kinase activity / cell competition in a multicellular organism / virion component => GO:0044423 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / viral release from host cell by cytolysis / positive regulation of gluconeogenesis / viral life cycle / peptidoglycan catabolic process / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / cell wall macromolecule catabolic process / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / lysozyme / lysozyme activity / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / chromosome, telomeric region / damaged DNA binding / non-specific serine/threonine protein kinase / protein ubiquitination / defense response to bacterium / phosphorylation / DNA repair / protein serine kinase activity / apoptotic process / DNA damage response / host cell nucleus / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region ...Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Armadillo-like helical / Lysozyme-like domain superfamily / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Vpr protein / Endolysin / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5197288426 Å
AuthorsSchwefel, D. / Banchenko, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1851/1-1 Germany
CitationJournal: Plos Pathog. / Year: 2021
Title: Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.
Authors: Banchenko, S. / Krupp, F. / Gotthold, C. / Burger, J. / Graziadei, A. / O'Reilly, F.J. / Sinn, L. / Ruda, O. / Rappsilber, J. / Spahn, C.M.T. / Mielke, T. / Taylor, I.A. / Schwefel, D.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: 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
A: DNA damage-binding protein 1
B: DDB1- and CUL4-associated factor 1
C: Vpr protein fused to T4 lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,62412
Polymers197,8213
Non-polymers8029
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-23 kcal/mol
Surface area72430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.898, 95.540, 98.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127241.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 40876.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#3: Protein Vpr protein fused to T4 lysozyme / Lysis protein / Lysozyme / Muramidase


Mass: 29703.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Simian immunodeficiency virus
Gene: vpr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P00720, UniProt: A4UDG5, lysozyme

-
Non-polymers , 3 types, 262 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.
PH range: 7.8-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→79.07 Å / Num. obs: 85560 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 54.6751512341 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.78
Reflection shellResolution: 2.52→2.56 Å / Num. unique obs: 6264 / CC1/2: 0.48

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSXDSAPPdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZUE, 1QT6

6zue

1qt6


Resolution: 2.5197288426→79.0659625889 Å / SU ML: 0.440095094398 / Cross valid method: FREE R-VALUE / σ(F): 1.32551474912 / Phase error: 29.4127757546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260498009517 3948 4.65522120555 %
Rwork0.216112029271 80860 -
obs0.218135520807 84808 99.1894831639 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.2991472108 Å2
Refinement stepCycle: LAST / Resolution: 2.5197288426→79.0659625889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13548 0 49 253 13850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042088631835713866
X-RAY DIFFRACTIONf_angle_d0.8108429397918769
X-RAY DIFFRACTIONf_chiral_restr0.04852752225732117
X-RAY DIFFRACTIONf_plane_restr0.004326236951832425
X-RAY DIFFRACTIONf_dihedral_angle_d23.64702607667215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.55050.4463746743111510.4111499802792729X-RAY DIFFRACTION96.5147453083
2.5505-2.58270.4092495559841570.3903387618712811X-RAY DIFFRACTION97.3433912758
2.5827-2.61670.3996917791341480.3786282965812771X-RAY DIFFRACTION98.1176470588
2.6167-2.65260.3830003438831360.3596700321662865X-RAY DIFFRACTION97.9758406791
2.6526-2.69050.3418074673511140.3541382009092825X-RAY DIFFRACTION98.0320213476
2.6905-2.73060.3826385785391300.3409352603352846X-RAY DIFFRACTION98.7392169874
2.7306-2.77330.4314440156571530.3406562284212793X-RAY DIFFRACTION98.4625668449
2.7733-2.81880.3529131711031350.3358484080682859X-RAY DIFFRACTION98.551678736
2.8188-2.86740.3282100971371250.3180207854932849X-RAY DIFFRACTION98.9683860233
2.8674-2.91950.3446947459971540.3081654113782884X-RAY DIFFRACTION99.5086799869
2.9195-2.97570.3581589803821220.2785906378482874X-RAY DIFFRACTION99.0740740741
2.9757-3.03640.3149681105911430.28156259162841X-RAY DIFFRACTION99.5330220147
3.0364-3.10250.3032979852751410.2595970614322892X-RAY DIFFRACTION99.4426229508
3.1025-3.17460.3245146963141460.2583287116562883X-RAY DIFFRACTION99.5399277029
3.1746-3.2540.275204217181630.242932842882833X-RAY DIFFRACTION99.5018266357
3.254-3.3420.2736821921051270.2257137552412918X-RAY DIFFRACTION99.640052356
3.342-3.44030.2958804397341590.227626209722836X-RAY DIFFRACTION99.5678191489
3.4403-3.55140.2786339794841580.2241496234872891X-RAY DIFFRACTION99.7383055283
3.5514-3.67830.2527121754641560.2152278366712903X-RAY DIFFRACTION99.8694090761
3.6783-3.82560.2357787050621400.2043211121792920X-RAY DIFFRACTION99.8043052838
3.8256-3.99970.2620619636151370.1906232710252889X-RAY DIFFRACTION99.8021108179
3.9997-4.21050.2465255951231370.1801499011372920X-RAY DIFFRACTION99.9346191566
4.2105-4.47430.2041298583291350.1577620669622954X-RAY DIFFRACTION99.9352960207
4.4743-4.81980.1789293795251450.146078120072922X-RAY DIFFRACTION100
4.8198-5.30470.17977992571250.1566128795352980X-RAY DIFFRACTION100
5.3047-6.07210.2249473439681240.1870201209212990X-RAY DIFFRACTION99.9678972713
6.0721-7.64920.2385266676991440.1948512925053022X-RAY DIFFRACTION99.8423210344
7.6492-79.06590.2061773637341430.1757186977633160X-RAY DIFFRACTION99.7282608696
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)
10.3593543672070.174360077235-0.1176574710220.299377895508-0.01530573179160.173712044947-0.04728969774490.06870381011490.133748704310.0149388652230.01071091582540.1742455509460.04140919127880.025939527399-0.001153484475350.274535768590.0150218773431-0.02298442260440.2643546592440.00769117203790.330721200658541.64521.52426.374
20.0093710474348-0.1154980881240.00527831801832-0.02697687567250.01939354116850.319133764876-0.14306459734-0.03476235466030.02364107619380.0402914691930.1640226371790.1113021651430.563773564539-0.1679555467890.1201896284280.59922432506-0.175246425547-0.1680059825960.385322847505-0.0819533060554-0.580832264728562.5770.085-22.724
30.3800600278430.261657838504-0.03427553825050.5563066005780.2359046004270.282282642152-0.005500071432870.06716657305430.0431985843462-0.07130594729560.106476580835-0.07651464322290.00481192400684-0.01328663259610.01638308839920.2191906190750.007616166681520.01441063831920.2819868381880.01360198373450.240391709307573.82418.68517.827
40.00285477712690.00884390103869-0.00182531631120.00710640180693-0.003824899043840.000766163524193-0.0974295771660.02115155348350.107287951172-0.0457345555551-0.0590871660941-0.0457382815260.118164581681-0.1641766001072.92164813879E-70.363647200015-0.010554672346-0.009223454505640.429033583236-0.02330136025650.387145342653571.51926.02436.845
50.0164927068720.00917925358897-0.01385545880130.01472006135390.004978594459680.0151237852173-0.0721060253062-0.07104256569420.0603986073151-0.221366580956-0.0345763447346-0.141356404113-0.04653977055140.0627401258251-0.00068336281790.371194504166-0.040377604934-0.112290417470.372104289621-0.01035922404550.661402379864581.6658.20536.987
60.0122524205752-0.0297119683875-0.04003962505640.06342319873220.089614184280.16708761462-0.2659394628-0.2304078234520.3554303150970.0287277705349-0.1674405274510.219424636387-0.112320819419-0.256844403403-0.01698596972170.4135740892060.0984970309763-0.1710375871840.537549729916-0.2403124332060.877426916347559.42259.9645.13
70.00693010694476-0.0127396435932-0.003168552459020.01777075850830.006078724070780.00496504349247-0.176088170937-0.01934640102880.001001549923520.0505497385039-0.179408643510.07616861366040.0931932679088-0.1577762568165.06034339097E-80.5120469823650.03393045533650.1019427650810.513555751571-0.1306749876610.643085639903562.74543.41548.97
80.00337237215721-0.004584282665370.002793644759380.00805384184678-0.0009071057376190.000256036234982-0.0990840073028-0.0189795761760.03622675097040.0857439798833-0.0115796765773-0.0058187321266-0.0384945198508-0.04687177813582.92977816E-70.569122245815-0.001759909787250.03710693735150.378383621874-0.05804677443390.494238690102574.17939.00548.113
90.0217518957591-9.18344025469E-50.009844643169580.00523616259995-0.005189564714130.01509036354-0.0484438710976-0.0664244311231-0.0866455870930.1489318865030.00164757581222-0.1213928265320.01244448578710.135671237762-1.85047949516E-70.4375781011930.0144262435383-0.138075980520.3686555465450.01665881791020.562844833531585.49240.36243.595
100.03045922055860.0679049987810.004879669457350.40618011449-0.07161242803050.3374500129940.09344255846990.104343507144-0.162219964055-0.376579055982-0.463391272811-0.109184305356-0.0564290511226-0.028036761397-0.2723857774760.7067825697490.1669963281190.1277958015870.5166068578290.01212779257830.612192096987590.17264.9467.051
110.008191145707470.0134302491750.00510573746840.0122689194656-0.0005690010184120.00405104812366-0.114203526223-0.05432754286210.113029315411-0.09446468027149.54162473901E-5-0.02451991877-0.030014775839-0.06574830808127.441349050870.611039445565-0.0976070724803-0.1910509847840.466255271473-0.03510905567160.672824667499591.42771.38745.886
120.0742405058805-0.0087167855931-0.02863373707180.0234104034355-0.01764738970970.054463601828-0.0390590473553-0.0391619535378-0.0341111345130.0391552734179-0.1288182026740.01373295464330.004200303606750.0448006494607-0.04847486115580.304544402476-0.087777880628-0.09397383186750.499723345241-0.1295167550210.605141507412592.66363.9355.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:365 )A-1 - 365
2X-RAY DIFFRACTION2( CHAIN A AND RESID 366:698 )A366 - 698
3X-RAY DIFFRACTION3( CHAIN A AND RESID 699:1140 )A699 - 1140
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1046:1086 )B1046 - 1086
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1087:1171 )B1087 - 1171
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1172:1264 )B1172 - 1264
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1265:1332 )B1265 - 1332
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1333:1359 )B1333 - 1359
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1360:1399 )B1360 - 1399
10X-RAY DIFFRACTION10( CHAIN C AND RESID -165:4 )C-165 - 4
11X-RAY DIFFRACTION11( CHAIN C AND RESID 5:37 )C5 - 37
12X-RAY DIFFRACTION12( CHAIN C AND RESID 38:91 )C38 - 91

+
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://pdbjlvh1.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