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- PDB-9nfq: Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 -

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Basic information

Entry
Database: PDB / ID: 9nfq
TitleCrystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7
Components
  • DNA damage-binding protein 1
  • Protein cereblon
  • Serine/threonine-protein kinase Nek7
KeywordsDNA Binding Protein/Transferase / Ternary complex / Molecular glue degrader / neosubstrate / DNA Binding Protein-Transferase complex
Function / homology
Function and homology information


NEK6-subfamily protein kinase / negative regulation of monoatomic ion transmembrane transport / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair ...NEK6-subfamily protein kinase / negative regulation of monoatomic ion transmembrane transport / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation by virus of viral protein levels in host cell / 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 / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of telomere maintenance / microtubule organizing center / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / spindle assembly / positive regulation of gluconeogenesis / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / molecular function activator activity / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / spindle pole / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / chromosome, telomeric region / protein ubiquitination / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / centrosome / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / RSE1/DDB1/CPSF1 second beta-propeller ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / ADENOSINE-5'-DIPHOSPHATE / DNA damage-binding protein 1 / Serine/threonine-protein kinase Nek7 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsQuan, C. / Petzold, G. / Bunker, R.D. / Wiedmer, L. / Gainza, P. / Tsai, J.H.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mining the CRBN Target Space Redefines Rules for Molecular Glue-induced Neosubstrate Recognition
Authors: Petzold, G. / Gainza, P. / Annunziato, S. / Lamberto, I. / Trenh, P. / McAllister, L.A. / DeMarco, B. / Schwander, L. / Bunker, R.D. / Zlotosch, M. / SriRamaratnam, R. / Gilberto, S. / ...Authors: Petzold, G. / Gainza, P. / Annunziato, S. / Lamberto, I. / Trenh, P. / McAllister, L.A. / DeMarco, B. / Schwander, L. / Bunker, R.D. / Zlotosch, M. / SriRamaratnam, R. / Gilberto, S. / Langousis, G. / Donckele, E.J. / Quan, C. / Strande, V. / De Donatis, G.M. / Alabi, S.B. / Alers, J. / Matysik, M. / Staehly, C. / Dubois, A. / Osmont, A. / Garskovas, M. / Lyon, D. / Wiedmer, L. / Oleinikovas, V. / Lieberherr, R. / Rubin, N.T. / Lam, D.T. / Ilic-Widlund, N. / Ritzen, A. / Caceres, R.M. / Vigil, D. / Tsai, J.H.C. / Wallace, O. / Peluso, M. / Sadok, A. / Paterson, A.M. / Zarayskiy, V. / Fasching, B. / Bonenfant, D. / Warmuth, M. / Castle, J. / Townson, S.A.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Protein cereblon
C: Serine/threonine-protein kinase Nek7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,6327
Polymers212,5423
Non-polymers1,0904
Water00
1
C: Serine/threonine-protein kinase Nek7
hetero molecules

A: DNA damage-binding protein 1
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,6327
Polymers212,5423
Non-polymers1,0904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area8610 Å2
ΔGint-57 kcal/mol
Surface area62260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.579, 121.857, 144.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)

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Components

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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: 127097.469 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 Protein cereblon


Mass: 50603.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#3: Protein Serine/threonine-protein kinase Nek7 / Never in mitosis A-related kinase 7 / NimA-related protein kinase 7


Mass: 34841.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TDX7, NEK6-subfamily protein kinase

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-A1BX6 / (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide


Mass: 572.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H28N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.25→46.61 Å / Num. obs: 24342 / % possible obs: 94.3 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.236 / Net I/σ(I): 7.3
Reflection shellResolution: 3.25→3.4 Å / Num. unique obs: 1478 / CC1/2: 0.612

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Processing

Software
NameVersionClassification
PHENIXdev_5430refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→46.61 Å / SU ML: 0.4214 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 1184 4.87 %
Rwork0.2116 23152 -
obs0.2141 24336 72.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.44 Å2
Refinement stepCycle: LAST / Resolution: 3.25→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11499 0 70 0 11569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010711804
X-RAY DIFFRACTIONf_angle_d1.309215994
X-RAY DIFFRACTIONf_chiral_restr0.0911799
X-RAY DIFFRACTIONf_plane_restr0.00522082
X-RAY DIFFRACTIONf_dihedral_angle_d13.40464419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.40.362590.2871478X-RAY DIFFRACTION36.93
3.4-3.580.3246850.25971831X-RAY DIFFRACTION46.29
3.58-3.80.29481180.2462236X-RAY DIFFRACTION56.68
3.8-4.090.30081560.23412668X-RAY DIFFRACTION67.8
4.09-4.510.26061810.19373244X-RAY DIFFRACTION81.9
4.51-5.160.23381940.18993590X-RAY DIFFRACTION89.82
5.16-6.490.28971950.22553931X-RAY DIFFRACTION97.22
6.5-46.610.21911960.19384174X-RAY DIFFRACTION98.53
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)
12.2935080271422-0.23673947805462-0.389129422012942.19298125106980.380572468747982.5607427328319-0.54893278220635-0.278839043649810.488748600433050.947114817204150.28349221136799-1.2754951400632-0.415422348697440.40519763675120.11189954938660.71425998107052-0.032716818102525-0.71473825326430.464346618854-0.0153838286608531.252235254855213.94899778662586.26191183253551.683042419605
23.1824601669594-0.728419171529760.345961549094874.5364151956461-0.202377952803452.1040097779435-0.157238961370240.64410671026693-0.29439315454356-0.68954221876126-0.00181307327330560.0998937823780030.040927169959319-0.0234074051266570.146011247466920.29603412252518-0.10689901889257-0.0505363773035110.54426803117793-0.0398143416940050.34638242210338-5.467862371518667.31554869707625.736526644827
34.1960924801447-0.10001336332657-0.945275252412763.0076040768552-1.38527471227374.66895494086620.279691799683621.02900684681730.3722354860653-0.49666203236279-0.16380481878682-0.51904006271207-0.24961665536780.55777073197986-0.112026105686670.51156562974222-0.0632327857377560.240511339270941.23693617039370.272337725631381.489829562675927.45594462947175.19107146442719.940017358578
47.4317380189521-1.799503933968-1.53261370088777.8001964350225-1.69438689781757.3618841364736-0.47027119893639-0.47811975362094-0.46821364867502-0.066902697299129-0.070234733041872-0.776902296909581.20967268507570.484581223267590.409759806964560.564438701042580.0621910103816740.164476570794680.46596336909689-0.0618850348006580.5569060606743722.24093386645830.90319691070550.995505179198
56.116419996025-6.67395307349510.0553369730636619.5657623826334-0.714650462189771.698895549027-0.56507553789021-0.7278128951576-0.0916940033193231.43772328301950.2501840512774-0.012451816098754-0.095619733220398-0.804673033719640.381388200007440.72989740613914-0.049838415785341-0.135170191098730.74593538833488-0.103537384404340.708141341947760.5119082634967265.20434130395152.225317941675
63.0716500924313-1.71729029119931.88567936333237.9622422337749-1.53721923804471.7414073490259-0.16912273684222-0.0738964009928560.0257458543420450.492093955379080.19206570016774-0.86933733877871-0.01561779469844-0.21483289437947-0.0928307014712420.23483720565766-0.0388341932073380.124559894608620.3601185776465-0.110663845286530.675017255797690.5106652861387349.59928517728947.344063753412
72.7543598195163-0.41624641640028-0.313396195580158.5889457487915-0.375007911373272.52286393129260.50453131247573-0.4950453173351-0.820794604906651.70771897867790.129480479347040.461612665480640.62167672866998-0.21642333071355-0.512368989750880.83087907667264-0.10395681839708-0.0199359593373050.529136264170650.126235972966661.0359362882651-4.78002187386224.03217969541753.404137325787
86.00428382704841.4869836400875-1.72738050237475.8401511390057-2.42458560954176.89668650726360.45211144462777-0.24923138456663-0.0577644028556081.40670319681660.335521395249630.48198439699213-0.61996622050174-0.72479456701678-1.27497255243250.815880187100430.0377414705469910.347205073286640.35447249406825-0.040833476547581.1271243221811-8.15489829290630.70370099995950.019762779786
91.1823032880979-0.1175674315507-0.0180920503821611.11018386330820.162389830970691.15341051523260.0185378134694870.0097948393259822-0.0590333026883710.62734380859782-0.346640854802-0.823379540450760.170312163310950.183153094965460.223127835254911.0596061682729-0.11842036796476-0.426740699581240.416322928030960.16398700100821.56446220788957.59072640695893.342219403332546.407306704199
102.4832901816585-1.37368817144390.787765087201584.74212850633640.786974538698282.86518059080570.52359660168380.00753084212871210.20312152009944-0.50342354768017-0.167372541771780.41892173195969-0.56773824997479-0.066142451930423-0.232667627492831.0346426466775-0.019800346186057-0.222476179922560.505421264065810.0386771116954391.0975435876058-8.27709687460050.4863369756476239.945098426588
111.57698161587810.330311627299652.08160949826280.319830282191380.395264636868083.0470783139043-0.432811335885190.449759868602350.39660385783818-0.31861361597986-0.38741690849897-0.24752021845941-1.21609689062730.45604476845681-0.283127510585551.036707870245-0.030340627507381-0.252244755826950.50332209130807-0.0137954171350011.1722556797239-9.1769131208823-0.6841058344001537.979682589825
122.0700184443182-1.51473493683291.3579107871193.5638621472295-0.0329704679707681.46071364239160.213530216721510.517641021895880.25655853018992-1.6784817247361-0.25778785645873-0.8342424498303-0.728204009800611.5761810036464-0.00700221609376421.1418658008944-0.246160745812620.0235366653367960.845932957147080.0455722134860831.1983870542367-2.296862944783-15.44647212083828.086608347712
130.735251015999370.634758448221040.0751135432174783.0366664286461-1.09965276371342.34893083857940.136238479280980.0071752843270129-0.1697212600608-0.035095745343465-0.471507314675360.83967758630008-0.843465579613990.56463940091255-0.416484355533940.72879414232934-0.090380794060121-0.345233549561680.522418719966240.157831026970671.7534639471396-14.705863483191-17.22707807357433.291640620429
146.3722290002261-3.7617838236268-3.75154685725922.360069350441.92121828962192.8159262077343-0.079759437929721.4480267455014-0.27635474846604-1.0662732546512-0.00328818822785731.7228248091523-0.4890528614825-1.1547936023120.255932138966391.1553758661155-0.10145263629807-0.726022969329781.0525911912334-0.0592127315127281.7402194008719-25.607602976934-7.919925546195430.737511295507
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 336 )AA1 - 3361 - 336
22chain 'A' and (resid 337 through 1044 )AA337 - 1044337 - 712
33chain 'A' and (resid 1045 through 1140 )AA1045 - 1140713 - 804
44chain 'B' and (resid 64 through 178 )BB64 - 1781 - 115
55chain 'B' and (resid 179 through 225 )BB179 - 225116 - 162
66chain 'B' and (resid 226 through 311 )BB226 - 311163 - 248
77chain 'B' and (resid 312 through 404 )BB312 - 404249 - 335
88chain 'B' and (resid 405 through 442 )BB405 - 442336 - 366
99chain 'C' and (resid 20 through 72 )CD20 - 721 - 53
1010chain 'C' and (resid 73 through 154 )CD73 - 15454 - 135
1111chain 'C' and (resid 155 through 182 )CD155 - 182136 - 163
1212chain 'C' and (resid 183 through 214 )CD183 - 214164 - 195
1313chain 'C' and (resid 215 through 252 )CD215 - 252196 - 233
1414chain 'C' and (resid 253 through 300 )CD253 - 300234 - 281

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  • 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

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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

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