[English] 日本語
Yorodumi
- PDB-6zhs: Uba1 bound to two E2 (Ubc13) molecules -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zhs
TitleUba1 bound to two E2 (Ubc13) molecules
Components
  • Ubiquitin-activating enzyme E1 1
  • Ubiquitin-conjugating enzyme E2 13
KeywordsLIGASE / Ubiquitin / E1 / Ubc13
Function / homology
Function and homology information


protein targeting to vacuolar membrane / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin conjugating enzyme complex / ubiquitin activating enzyme activity / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins ...protein targeting to vacuolar membrane / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin conjugating enzyme complex / ubiquitin activating enzyme activity / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / protein polyubiquitination / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain ...Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin-activating enzyme E1 1 / Ubiquitin-conjugating enzyme E2 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMisra, M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHI 425-6/1 Germany
CitationJournal: To Be Published
Title: ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system.
Authors: Misra, M. / Schaefer, A. / Kuhn, M. / Pluska, L. / Tessmer, I. / Sommer, T. / Schindelin, H.
History
DepositionJun 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-conjugating enzyme E2 13
C: Ubiquitin-conjugating enzyme E2 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,23311
Polymers149,4883
Non-polymers7458
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-66 kcal/mol
Surface area56510 Å2
Unit cell
Length a, b, c (Å)177.710, 72.900, 139.520
Angle α, β, γ (deg.)90.000, 112.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

-
Components

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 114393.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: UBA1, YKL210W / Production host: Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme
#2: Protein Ubiquitin-conjugating enzyme E2 13 / E2 ubiquitin-conjugating enzyme 13 / Ubiquitin carrier protein 13 / Ubiquitin-protein ligase 13


Mass: 17547.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli (E. coli)
References: UniProt: P52490, E2 ubiquitin-conjugating enzyme
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, HEPES, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. obs: 67708 / % possible obs: 66.13 % / Redundancy: 5.6 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 0.987 / Net I/σ(I): 6.97
Reflection shellResolution: 2.35→2.435 Å / Num. unique obs: 398 / CC1/2: 0.424

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMM

3cmm


Resolution: 2.35→24.92 Å / SU ML: 0.3688 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 32.5974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 2266 4.97 %RANDOM
Rwork0.2157 43323 --
obs0.2188 45589 66.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.78 Å2
Refinement stepCycle: LAST / Resolution: 2.35→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10283 0 46 307 10636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002710599
X-RAY DIFFRACTIONf_angle_d0.632514358
X-RAY DIFFRACTIONf_chiral_restr0.04261590
X-RAY DIFFRACTIONf_plane_restr0.00441875
X-RAY DIFFRACTIONf_dihedral_angle_d22.21293988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.40970.4469149X-RAY DIFFRACTION3.67
2.4-2.460.508170.3812445X-RAY DIFFRACTION10.96
2.46-2.520.4158460.3422879X-RAY DIFFRACTION21.56
2.52-2.590.3558580.31681387X-RAY DIFFRACTION33.86
2.59-2.660.3841820.31721776X-RAY DIFFRACTION43.44
2.66-2.750.40151010.32492080X-RAY DIFFRACTION50.96
2.75-2.850.3971420.29752445X-RAY DIFFRACTION60.81
2.85-2.960.35371440.27472883X-RAY DIFFRACTION70.35
2.96-3.10.33621730.26493259X-RAY DIFFRACTION79.8
3.1-3.260.33961950.25033668X-RAY DIFFRACTION90.26
3.26-3.460.29162100.2174011X-RAY DIFFRACTION97.84
3.46-3.730.28392250.19333989X-RAY DIFFRACTION97.66
3.73-4.10.23032020.17244071X-RAY DIFFRACTION99.19
4.1-4.690.21112230.16214058X-RAY DIFFRACTION98.89
4.69-5.90.22222180.18794060X-RAY DIFFRACTION98.12
5.9-24.920.2332230.214163X-RAY DIFFRACTION98.47
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)
11.685924869820.509396905158-0.3580366769551.61032181493-0.1955732392042.97992337806-0.00579614382883-0.07415817925190.5658765554270.1178119330750.04636341564920.113926494684-0.5220453191-0.144994367111-0.06728097264150.2506717745380.02715671885460.009204901932380.151259850008-0.01034611357630.163280849488-10.6773910715.4304070230353.2876445226
22.200468926330.436543286548-0.4431296771410.560649276221-0.5178410823730.7161427777380.12713029079-0.0853962636684-0.1523216494460.0981163538452-0.0320624777665-0.03913678202160.0290520606149-0.0274970293543-0.03178914597420.150636530748-0.0225656462692-0.06627809213310.2238313612650.00841478657110.15616631145-12.4767257764-14.99449298657.7649188988
34.827880763181.431187065661.534438586834.699725074411.045740390554.413073899020.1592661097240.0318238372342-0.6469822433360.0771002844525-0.0165904417564-0.09593068133370.412335490803-0.161772632883-0.06062137329290.103073885-0.0283466451195-0.01160430891290.2458088408950.0504681992560.132741285962-33.0509077449-32.339701707257.1225475916
41.535346564770.02662752650190.1153356495811.00326312409-0.1389912577081.893762008520.06387373404130.1216054771750.00527548349125-0.1334743975190.0453841552298-0.0407661366264-0.109501962180.0908450396888-0.02693573860810.130650634723-0.030833973217-0.01854824059710.2046464091610.01893900839160.12731270348-0.364760691377-5.2798341501339.6325415374
50.7550108337920.0702116950703-0.32605721689-0.0214024421962-0.03636684293160.136917846593-0.1836933070180.437550838181-0.429769969126-0.05161891256360.0498818494190.0352397742527-0.022643979257-0.0584811600275-0.05794188910210.22323077863-0.022374989833-0.05381260025780.459992588181-0.03362211671010.0942717390322-26.0398709244-15.676482882429.1311444894
61.543849316490.05790860904610.3337128671082.55129769791-0.2760886232861.39538698009-0.07174162299570.512502367597-0.0423430550124-0.697958535771-0.02715845628210.1304777826560.0197987091027-0.266099993325-0.02847215641970.1166638886740.0720604633964-0.1011629563830.5387443098790.09801878357090.0655564632495-56.775375067-12.177896407632.4610536685
72.16316024856-0.2673805926060.02207785129483.12715916948-0.7146703335283.23478814876-0.0229829684240.3994983015870.301776663361-0.2181417635820.1028757789440.472468179254-0.361378336804-0.469494598350.09700837691680.2383890293250.0585819195614-0.07689955988350.4695442278410.1085790849160.269905980026-58.9534682384-0.74342678597735.6035019837
81.942488118820.176204632107-0.430233743839-0.0521436959836-0.04782913105840.07833729472470.1068277574160.09703876674540.212059852733-0.09632646951970.00706299715282-0.0902761355519-0.202238390457-0.03429797116060.1327923428160.1219418472720.0182858452237-0.09012448962560.3428188065680.05905514572280.130085860112-32.6582834081-6.6831121112939.115225381
91.51012624884-0.08380662186050.8922876755310.7964570701590.8835443575562.68279385237-0.02650910671960.670979065628-0.255643861529-0.296377508030.093087482705-0.02423052226780.1396229341460.0546582612765-0.08534752016840.33046094258-0.148643309341-0.0003221193927730.566398239428-0.05858113224250.12793192488-15.6481777268-21.64761686617.81340356332
104.329136727490.87475068733-2.933901106732.76198579679-1.08084989533.14341749617-0.2638975711880.264915412472-0.229914781556-0.4280869433140.0245859364419-0.2893307013290.4150077693820.7047787337090.1861371630.404744890296-0.08922762575280.1104896668940.737355138835-0.01566361764460.165858454603-25.9033588834-28.440136063611.4397613448
115.319052497870.575922177815-0.9959374520131.388123109810.3626658916962.60175432712-0.1817222575610.8024045340790.101264538211-0.5175668284250.1086811046250.1651994149480.2876770040070.106236582302-0.01010209230050.391415098785-0.03411224897760.02728460701330.578568117698-0.1192247043250.14922152344-38.4240794761-27.83797370468.82449410905
125.842202484060.567837610192-2.372096354921.69440635039-1.607156891753.14775862176-0.333895308810.5198845829490.0328350771936-0.3772080725680.345083003651-0.00330920612287-0.0166000307107-0.06088597927460.07662622340220.305252423855-0.05821879861320.01820008684610.460518407865-0.04113189673330.160797623494-42.5988166381-30.199963805916.6694926593
135.859583196390.391895147017-1.491173712140.735508687286-0.6558264043833.4229851783-0.134340549410.2008760488810.37609160334-0.269649557070.07407777623330.0653268686392-0.446154487421-0.0599411338118-0.2313705536990.286540413872-0.0652495490145-0.03015723218320.402522179988-0.1106324372770.0646551610951-50.7900122937-26.240809081921.1826307134
146.897622339780.986628731602-2.484562570280.441829792748-0.8922535648093.05717278210.303689275254-1.38378605705-0.2107362143480.167306080492-0.143511943664-0.174765202577-0.07416643966230.4095227140060.1789700573330.368509250509-0.06555677676650.01201734946060.693956707022-0.09567096226890.237963792057-35.0013433251-30.067215148326.2085433081
154.859161481581.12710028882-1.491470534241.26931307523-0.9156751957742.56847247753-0.331650485876-0.673625667277-0.24087578113-0.2750726818890.152896711522-0.07897448607980.125348821927-0.001274972159780.01766020318860.164483239653-0.00744946991835-0.009942311411920.329796463483-0.07818873507960.107775604275-49.324614304-34.892782541225.593009595
164.000874758020.373622463331-1.431523881173.38549477928-2.020293341781.66221359995-0.2038153046111.44327861829-0.21181107338-0.5807692369020.184166382042-0.1335373253340.28062687103-0.410328133081-0.04017593513580.220039883723-0.189703860548-0.0445021374530.858648568221-0.04798745906610.195166182681-60.344509082-36.057482204115.9509622378
177.46986298631-0.3999286392711.26183671415.8317967642-0.1631202333754.768536306520.130988006726-0.202091816524-0.1362714442940.5316649285270.450883584087-0.5465209263230.2114856506270.765947980024-0.2755141921890.1944186942790.1149020319690.02561912265610.550997458396-0.1407357162320.69524151087512.8031622465-41.870797190147.9197701205
185.31136917819-0.08745625149682.714654239432.52109358664-0.03026566844684.56466022991-0.04117207387630.220164825361-0.600477630407-0.1981345482120.0977734888875-0.106078252149-0.0530888600820.216554569744-0.06441539188680.2839637390860.0152861801188-0.01065042717440.18876317698-0.09281907732770.4264244466920.0329660453915-37.390108799838.2128255043
196.465165608510.5657294522881.549672282563.91546660132-0.9426793329857.36246675660.254885660199-0.9351106148240.4418436217170.3027889815670.1626581788680.406336057024-0.762490737418-0.483220069550.4736506115270.2417632584840.0248917719655-0.001799846176120.55951705547-0.1230060117420.521130251891-12.7767496256-32.50742063539.168416817
207.8203661416-0.5405662675084.760820101672.96270526906-0.7523030085216.459865274410.0141765482385-1.32927885619-0.6990466657930.6710182375930.4421620991130.2957952704090.648241438943-1.29862387785-0.3635568972950.64034434146-0.0377977596368-0.04346215852880.5038122160330.1691619313560.65121375279-5.31461807656-42.001873601750.9360791189
214.336399786010.1980606544163.754862553263.750564675690.1061024865153.920973072250.178219736506-0.447864790379-0.2481018083980.232818194125-0.0956005128320.374444902038-0.0319991992613-0.38432929496-0.05249810762990.335968824802-0.0502023910530.04278705089690.241507835192-0.08811753495110.835346517476-11.1543403572-42.107084569941.1791249508
227.29923344290.542334637153.04373062413.17028286168-0.423622385975.59237090097-0.3813928686880.215468055971-0.191079450952-0.3691105850960.08581364308470.361830033269-0.0228659399025-0.346346521563-0.04976053857930.342989382095-0.0220502558036-0.09855530525440.251443448061-0.06639263138310.45837773775-17.3774235436-37.769356324427.8431854372
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 122 )AA10 - 1221 - 113
22chain 'A' and (resid 123 through 200 )AA123 - 200114 - 191
33chain 'A' and (resid 201 through 264 )AA201 - 264192 - 255
44chain 'A' and (resid 265 through 545 )AA265 - 545256 - 538
55chain 'A' and (resid 546 through 624 )AA546 - 624539 - 619
66chain 'A' and (resid 625 through 724 )AA625 - 724620 - 719
77chain 'A' and (resid 725 through 813 )AA725 - 813720 - 787
88chain 'A' and (resid 814 through 885 )AA814 - 885788 - 859
99chain 'A' and (resid 886 through 1024 )AA886 - 1024860 - 998
1010chain 'B' and (resid 0 through 17 )BB0 - 171 - 18
1111chain 'B' and (resid 18 through 40 )BB18 - 4019 - 44
1212chain 'B' and (resid 41 through 67 )BB41 - 6745 - 71
1313chain 'B' and (resid 68 through 86 )BB68 - 8672 - 91
1414chain 'B' and (resid 87 through 100 )BB87 - 10094 - 107
1515chain 'B' and (resid 101 through 132 )BB101 - 132108 - 142
1616chain 'B' and (resid 133 through 151 )BB133 - 151143 - 161
1717chain 'C' and (resid 1 through 17 )CC1 - 171 - 17
1818chain 'C' and (resid 18 through 76 )CC18 - 7618 - 76
1919chain 'C' and (resid 77 through 86 )CC77 - 8677 - 86
2020chain 'C' and (resid 87 through 100 )CC87 - 10087 - 100
2121chain 'C' and (resid 101 through 124 )CC101 - 124101 - 124
2222chain 'C' and (resid 125 through 151 )CC125 - 151125 - 151

+
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