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- PDB-7mpq: Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ -

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Basic information

Entry
Database: PDB / ID: 7mpq
TitleBartonella henselae NrnC cleaving pGG in the presence of Mn2+
Components
  • 5'-phosphorylated GG
  • NanoRNase C
KeywordsRNA BINDING PROTEIN / RNase / bacteria / enzyme
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / : / RNA / 3'-5' exonuclease
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI142400 United States
CitationJournal: Elife / Year: 2021
Title: Structural characterization of NrnC identifies unifying features of dinucleotidases.
Authors: Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /
Abstract: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NanoRNase C
C: NanoRNase C
E: NanoRNase C
G: NanoRNase C
I: NanoRNase C
K: NanoRNase C
M: NanoRNase C
O: NanoRNase C
R: 5'-phosphorylated GG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,18339
Polymers188,2199
Non-polymers5,96430
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33030 Å2
ΔGint-270 kcal/mol
Surface area62860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.681, 127.799, 128.809
Angle α, β, γ (deg.)90.000, 94.872, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
NanoRNase C


Mass: 23446.725 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BM1374165_00260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5MEI1
#2: RNA chain 5'-phosphorylated GG


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Succinic acid; 10% PEG 3,350; 20% xylitol, 5 mM MnCl2 (soak)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.8917 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8917 Å / Relative weight: 1
ReflectionResolution: 2.35→128.34 Å / Num. obs: 174471 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.67 Å2
Details: The 174471 reflections were counted with Friedel pairs separated. The number of reflections listed for refinement was calculated after merging Friedel pairs.
CC1/2: 0.994 / Net I/σ(I): 11
Reflection shellResolution: 2.35→2.38 Å / Num. unique obs: 12956 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.17_3644refinement
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3
Resolution: 2.35→128.34 Å / SU ML: 0.3232 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 4387 4.66 %
Rwork0.1619 89791 -
obs0.1639 94178 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.7 Å2
Refinement stepCycle: LAST / Resolution: 2.35→128.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13055 47 352 622 14076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006813882
X-RAY DIFFRACTIONf_angle_d0.857618892
X-RAY DIFFRACTIONf_chiral_restr0.05042147
X-RAY DIFFRACTIONf_plane_restr0.00472404
X-RAY DIFFRACTIONf_dihedral_angle_d20.30355222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.33541270.29242373X-RAY DIFFRACTION77.42
2.38-2.40.37761730.27832975X-RAY DIFFRACTION98.19
2.4-2.430.35221480.27192970X-RAY DIFFRACTION98.11
2.43-2.460.32881500.24612991X-RAY DIFFRACTION98.34
2.46-2.50.27381600.22263015X-RAY DIFFRACTION99
2.5-2.530.27261560.20373016X-RAY DIFFRACTION98.97
2.53-2.570.26411420.19953013X-RAY DIFFRACTION98.75
2.57-2.610.27311460.19422969X-RAY DIFFRACTION98.58
2.61-2.650.27931510.19563032X-RAY DIFFRACTION98.48
2.65-2.690.31641220.20782994X-RAY DIFFRACTION98.61
2.69-2.740.2891420.21173043X-RAY DIFFRACTION98.33
2.74-2.790.25631470.20293004X-RAY DIFFRACTION98.53
2.79-2.840.25141520.21132966X-RAY DIFFRACTION97.38
2.84-2.90.29671490.20573005X-RAY DIFFRACTION99.15
2.9-2.960.25811420.20013031X-RAY DIFFRACTION99.37
2.96-3.030.29371430.19453040X-RAY DIFFRACTION99.28
3.03-3.10.23681370.18513040X-RAY DIFFRACTION99
3.1-3.190.22661280.18913024X-RAY DIFFRACTION98.75
3.19-3.280.2261470.17673017X-RAY DIFFRACTION98.17
3.28-3.390.22271440.1863006X-RAY DIFFRACTION98.25
3.39-3.510.2321630.17192907X-RAY DIFFRACTION96.69
3.51-3.650.22411610.15233050X-RAY DIFFRACTION99.07
3.65-3.820.2211580.14273021X-RAY DIFFRACTION99.31
3.82-4.020.14441500.13153057X-RAY DIFFRACTION99.23
4.02-4.270.14711450.11913016X-RAY DIFFRACTION98.84
4.27-4.60.1451690.11392981X-RAY DIFFRACTION97.92
4.6-5.060.16151250.11573007X-RAY DIFFRACTION96.73
5.06-5.790.16981100.14363104X-RAY DIFFRACTION99.69
5.79-7.30.16841470.15323083X-RAY DIFFRACTION99.42
7.3-128.340.13651530.13663041X-RAY DIFFRACTION96.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1192527225210.2891412499510.2979638953570.4326920892270.666524883661.755449172850.00211379319872-0.01567719937650.000285577679844-0.0406188665954-0.02198476141680.0338868357785-0.132240579229-0.110049913808-3.65828646637E-50.2192960140940.02542498565650.006903787513320.2420773213940.004203635317280.20774211549727.565842745528.415745417715.8648831875
20.1902867346190.0895605954108-0.1867865230910.304598179607-0.07387040667380.129915872469-0.05307097062790.146833899876-0.5096901226470.149093675303-0.242331347040.1314611240170.743386417049-0.5550791875882.82518023972E-50.320974945313-0.05462204794290.00686584508540.331048819705-0.0376345246290.41698365766720.27883121715.37310412510.644050266
30.308762729338-0.25951104073-0.1420406627050.01677150385960.2794298849220.503177968726-0.00890022690797-0.0265726339148-0.01137934338070.02407864156860.01626162324250.015982178644-0.03039405807630.00161672223363-1.26081438104E-50.322461993245-0.0006775894272440.02021128542240.29282999004-0.005194816700480.2715267665334.485927302329.143619112725.9078653979
40.839087890247-0.4669911586920.6999759513730.904830046985-0.3628492759050.734560878579-0.0155710213904-0.0292814436666-0.02693670145460.1967911996330.02570819146390.0445335717311-0.07837624627330.00911555059695-1.30904863321E-50.2812531907670.0004463984119630.04192075418390.278498974335-0.01806723071840.24662068707624.256004826423.296119989359.5691913931
50.720020175189-0.3895415864590.2427131590830.614827748394-0.1076693621690.3283534214010.0697234328320.0730900556312-0.1153217317710.0185779883290.00300816279120.2921892442690.0445436722241-0.0217131455982-5.12875948667E-60.298898052885-0.01095646014120.01572103165180.3021466146450.0003024044045410.30442650378820.969773908511.036328738851.3550452887
60.4206309093450.07786734072880.09723737654190.512392686790.371622655513-0.04174044145670.113724044402-0.108500663328-0.003509704808610.101802205126-0.0213493918950.01172783836970.08443575521460.115292879771.0359291641E-70.32960382568-0.000136766845771-0.011886295920.3026454347950.02719604898610.2573006822335.99908846417.2168824001360.3820402199
70.2634305929170.312255942933-0.2323471367351.54426092905-0.1150651775230.3688308505380.02552814753450.04878504188090.018388329687-0.09480254273350.04627082356980.1457924242640.00782215171851-0.00957901586447-1.30919221708E-50.294917230319-0.0125808011843-0.01323878129860.275280556692-0.02343849293370.29611080250329.1304195059-13.93856443135.32552446512
80.397179658878-0.317521767989-0.04192936854970.284841972980.1182490941940.1410974412260.0359147787369-0.0102191558273-0.04674061627720.199665588280.0347172741180.484612989583-0.20600701562-0.05741975494499.48138639163E-50.319154190721-0.03137412361310.01764660940870.404764297789-0.005947255676940.37853318524820.6084960306-15.881547313612.778666749
90.37951520238-0.0529029089538-0.1596146258060.649982037476-0.09337856813980.05353779162190.08713918770510.03375119688790.0266150971037-0.133490116776-0.07311748198510.03112013741910.0218193117610.0501430728716-4.77510205436E-50.299861405635-0.02102682217770.04766164629830.269106682832-0.04789610219840.28680209312140.6141787572-2.718491808834.62870684382
100.6719151600410.1545650866080.5330282941090.4008885884410.2743873758451.94107042806-0.0974885338691-0.097513396648-0.026918201097-0.04349591816570.055872300118-0.00684141233722-0.2310660068360.1712705961647.51056391833E-50.27341193266-0.03189544743740.002864930796770.320951001365-0.01425211073890.26084585409561.569348377333.200756851537.8740283494
110.372204488566-0.229526043471-0.1905145939260.4851927536060.0627964196420.180161269662-0.168478378968-0.116470230806-0.148353118254-0.02925469203880.144220089688-0.1670578139840.219751337440.639855860346-0.0001651992757310.3264033309020.04932702855140.006785307130280.4558149875790.00932011535850.38290289140869.375098947925.540605944343.8588184279
120.7690822470420.03582588270990.353342569410.4359755499230.1490496938060.276468659446-0.101196587092-0.181486506364-0.0261488243969-0.1207478386490.07806012641160.0418771013755-0.1044304059840.07133945725378.98781930387E-50.305548894423-0.02531784847450.01077421344450.3092235526290.000747078463520.21780639967451.472664457629.649173014126.4910831935
130.331511353421-0.169332685123-0.3505651876740.3381091877250.2813035333441.15494728996-0.01891844439730.03714832618130.02638423732310.01899630514870.02535877708120.0910674118390.12843898752-0.0722479299384-1.99221109869E-50.329288864308-0.0304700546332-0.01390955723330.2829697929930.04598466444110.31880114386425.7495461123-24.419836096747.2023380789
140.4069710976-0.06460106052780.2739380877880.211633444387-0.1549909545650.239714562071-0.03963636391610.03937981077980.219770066047-0.2563215998280.1519350923480.0724785571246-0.2128914713-0.1932924047972.39042132197E-60.421979359274-0.0214559899376-0.03373240810120.3772568163460.09919207292620.56862120912817.4563771809-15.428048689948.0601849294
150.604728233158-0.394282034611-0.1691952019780.479071732985-0.3127810978190.5494268391570.02126730731390.1117244908930.0003457225030830.03844477726940.00584398082584-0.0260248466070.247808274310.007522092516283.01648944412E-50.38622299653-0.02019419172430.003343301790970.2913007768510.03919186488640.29547761401837.6728981999-25.851207220437.0892185498
160.462659480064-0.605392582024-0.3891832527260.834576408897-0.2239032839550.813120253684-0.0868881121301-0.123775592679-0.07376862551440.342238852163-0.0329184341345-0.115058411137-0.02597936026230.1097324344724.21757861474E-50.433166604929-0.00325919704659-0.1557240255550.3677411356620.09052311126820.45799684044162.723680124-7.4785363364467.9061672695
170.396587968482-0.1422965725880.0148696699995-0.0131958497442-0.0711533345173-0.1147819467290.1206423211110.0840243263022-0.1463087213630.2525059456160.09343054115440.01815724180690.003432630529890.003838375179234.62868171947E-50.44691773679-0.0135074450088-0.05915848493560.3692836379070.0637471127530.36870963001654.1491941726-0.22615685435368.3575729775
180.5514508271760.0170017956139-0.02792950805571.445184496040.1191528573050.4396017207390.0747191565540.0357917439802-0.01652791444030.122710732451-0.0631547777767-0.236666135652-0.08459930363530.05847775212561.95906869765E-50.241241929440.00760341820997-0.0528741855720.3196233470290.02391246308130.28112682474557.79581258025.2569906947358.2289595971
190.7939651929231.030136203590.06818373216621.503957112930.4318256262450.103733077478-0.07427782626070.0185645814722-0.073686413798-0.2254144105370.152656475344-0.232527324527-0.04152832417820.055179360265-4.03107523307E-50.277593251517-0.01555187609110.09741984535490.346953936159-0.07089714782650.33555541957864.4577805936.067491561643.72665971041
200.3931768647760.262711086744-0.1076680708690.1585588023520.03312056059820.222959478564-0.1587657569810.0958946471475-0.1571834300390.1781901628230.0486445718821-0.209555413273-0.01558964432370.202477226138-0.0003830868632320.273475505702-0.008208010860720.04730585297630.430116939759-0.08807519810690.42924189774471.972792456411.593034224312.1238744892
210.4763821148540.4007108776670.1153214589510.528550194320.1999530707050.388828928583-0.1551205813880.01557224697090.0570562601098-0.08127248291410.122545300438-0.1158184935420.1008728049590.02294755449279.45657671867E-60.345297004515-0.01261210013640.06991284506630.318777728875-0.04774412280880.33581980647853.7832006099-4.989200814036.23663304997
220.7950948874470.330887876514-0.7637932320370.622479601568-0.1000079766371.11650384647-0.083921417965-0.0268914968117-0.08060580326470.0768076686323-0.0315474958636-0.1989788290730.2415802969630.05473046337847.75309861244E-50.3166671392420.0833700072365-0.01206207429510.3091977670790.03161691342180.46300373101662.7504235134-28.299634620530.9005665078
230.2261122028570.04251505468760.04111804166420.1533716730310.0602437002460.113409249728-0.261056146921-0.10470202038-0.1404606581250.0589958707644-0.105743968123-0.55808184215-0.3249248454280.456470173699-0.0006473769028980.4004558144610.0485938938255-0.03651885629450.4572377515690.06546792200650.71898380568671.3439706171-20.620214577427.2538536806
240.7184222983230.0279858674757-0.4292728127850.4153076430420.1753226951020.379375332707-0.05032023339730.001775297629410.01529800187870.08398710065550.0554153390791-0.1403432447950.1612304680440.0311427976509-9.3137848551E-50.4150383816660.0183870598788-0.05582819128460.296526077790.0641463497040.40163407813550.7342517528-24.992868997140.7893651521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:129)
2X-RAY DIFFRACTION2(chain A and resid 130:149)
3X-RAY DIFFRACTION3(chain A and resid 150:206)
4X-RAY DIFFRACTION4(chain C and resid 2:96)
5X-RAY DIFFRACTION5(chain C and resid 97:161)
6X-RAY DIFFRACTION6(chain C and resid 162:206)
7X-RAY DIFFRACTION7(chain E and resid 2:131)
8X-RAY DIFFRACTION8(chain E and resid 132:161)
9X-RAY DIFFRACTION9(chain E and resid 162:206)
10X-RAY DIFFRACTION10(chain G and resid 2:129)
11X-RAY DIFFRACTION11(chain G and resid 130:160)
12X-RAY DIFFRACTION12(chain G and resid 161:206)
13X-RAY DIFFRACTION13(chain I and resid 2:129)
14X-RAY DIFFRACTION14(chain I and resid 130:160)
15X-RAY DIFFRACTION15(chain I and resid 161:206)
16X-RAY DIFFRACTION16(chain K and resid 2:62)
17X-RAY DIFFRACTION17(chain K and resid 63:106)
18X-RAY DIFFRACTION18(chain K and resid 107:206)
19X-RAY DIFFRACTION19(chain M and resid 3:129)
20X-RAY DIFFRACTION20(chain M and resid 130:160)
21X-RAY DIFFRACTION21(chain M and resid 161:206)
22X-RAY DIFFRACTION22(chain O and resid 3:129)
23X-RAY DIFFRACTION23(chain O and resid 130:161)
24X-RAY DIFFRACTION24(chain O and resid 162:206)

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