[English] 日本語
Yorodumi
- PDB-8buo: Structure of DDB1 bound to DS24-engaged CDK12-cyclin K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8buo
TitleStructure of DDB1 bound to DS24-engaged CDK12-cyclin K
Components
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
KeywordsLIGASE / kinase / cyclin / ubiquitin / degrader
Function / homology
Function and homology information


: / Recognition of DNA damage by PCNA-containing replication complex / cyclin K-CDK12 complex / cyclin K-CDK13 complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / nuclear cyclin-dependent protein kinase holoenzyme complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER ...: / Recognition of DNA damage by PCNA-containing replication complex / cyclin K-CDK12 complex / cyclin K-CDK13 complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / nuclear cyclin-dependent protein kinase holoenzyme complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / Neddylation / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / viral release from host cell / regulation of signal transduction / ectopic germ cell programmed cell death / proteasomal protein catabolic process / cyclin-dependent kinase / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of gluconeogenesis / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / RNA splicing / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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 / mRNA processing / 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 / rhythmic process / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein autophosphorylation / chromosome, telomeric region / damaged DNA binding / protein kinase activity / protein ubiquitination / nuclear speck / cell cycle / cell division / DNA repair / protein serine kinase activity / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / 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 / Cyclin, N-terminal ...Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / 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 / Cyclin, N-terminal / Cyclin, N-terminal domain / Quinoprotein alcohol dehydrogenase-like superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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
Chem-RLC / Cyclin-K / DNA damage-binding protein 1 / DNA damage-binding protein 1 / Cyclin-dependent kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsKozicka, Z. / Kempf, G. / Petzold, G. / Thoma, N.H.
Funding supportEuropean Union, Switzerland, 7items
OrganizationGrant numberCountry
European Research Council (ERC)666068European Union
Swiss National Science Foundation31003A_179541 Switzerland
Swiss National Science Foundation310030_301206 Switzerland
Swiss Cancer League4980-02-2020 Switzerland
Swiss National Science FoundationCRSII5_186230 Switzerland
Marie Sklodowska-Curie Actions, FragNET ITN765445European Union
Other private Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Design principles for cyclin K molecular glue degraders.
Authors: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / ...Authors: Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / Haussinger, D. / Winter, G.E. / Fischer, E.S. / Slabicki, M. / Gillingham, D. / Ebert, B.L. / Thoma, N.H.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,40438
Polymers496,5589
Non-polymers3,84629
Water00
1
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,83313
Polymers165,5193
Non-polymers1,31410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,64111
Polymers165,5193
Non-polymers1,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,92914
Polymers165,5193
Non-polymers1,41011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.800, 249.800, 218.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 393 or resid 709 through 1140))
d_2ens_1(chain "D" and (resid 1 through 393 or resid 709 through 1140))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1140))
d_1ens_2chain "B"
d_2ens_2chain "E"
d_3ens_2(chain "H" and (resid 715 through 1040 or resid 1101))
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLYGLYAA1 - 3935 - 397
d_12ens_1LYSLYSHISHISAA709 - 1140409 - 840
d_21ens_1METMETGLYGLYDD1 - 3935 - 397
d_22ens_1LYSLYSHISHISDD709 - 1140409 - 840
d_31ens_1METMETGLYGLYGG1 - 3935 - 397
d_32ens_1LYSLYSHISHISGG709 - 1140409 - 840
d_11ens_2THRTHRCYSCYSBB715 - 10397 - 331
d_12ens_2RLCRLCRLCRLCBO1101
d_21ens_2THRTHRCYSCYSEE715 - 10397 - 331
d_22ens_2RLCRLCRLCRLCEX1101
d_31ens_2THRTHRCYSCYSHH715 - 10397 - 331
d_32ens_2RLCRLCRLCRLCHGA1101
d_11ens_3THRTHRHISHISCC20 - 26724 - 271
d_21ens_3THRTHRHISHISFF20 - 26724 - 271
d_31ens_3THRTHRHISHISII20 - 26724 - 271

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.475732009471, -0.509248106431, 0.717178793092), (0.50806056843, 0.506493615894, 0.696662526526), (-0.718020552611, 0.695794928951, 0.0177736567515)-127.740347445, 80.0107532905, -108.172609074
2given(-0.515765574076, 0.495826512385, -0.698671555321), (-0.551424239229, 0.432010492845, 0.713651345169), (0.655680700485, 0.753341226595, 0.0505946175323)-179.468492884, -29.0590685892, 34.1220646016
3given(-0.50932622143, -0.517220933522, 0.687800338826), (0.495603186064, 0.477100256616, 0.725777395005), (-0.703536979929, 0.710533497496, 0.0133366716069)-129.495184166, 79.4668600859, -107.40925592
4given(-0.514828903444, 0.500018862102, -0.696370833479), (-0.540222180264, 0.441504320977, 0.71640346908), (0.665665979399, 0.745020182344, 0.0428220944232)-179.677163425, -28.5636302641, 34.2052853481
5given(-0.553480514583, -0.511290671513, 0.657450507036), (0.482106153685, 0.447007449966, 0.753497177336), (-0.679141352412, 0.734006940634, -0.00091353437157)-132.82849786, 80.07955101, -107.023317443
6given(-0.490012187783, 0.520078067434, -0.699576199994), (-0.524946841737, 0.464642589885, 0.713118557475), (0.69593021861, 0.716677101238, 0.0453328069496)-179.248059341, -28.7374572999, 36.8964333796

-
Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 ...DDB p127 subunit / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / 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: 93675.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ddb1, DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q3U1J4, UniProt: Q16531
#2: Protein Cyclin-dependent kinase 12 / Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 ...Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 / CDC2-related protein kinase 7 / Cell division protein kinase 12 / hCDK12


Mass: 40143.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK12, CRK7, CRKRS, KIAA0904 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#3: Protein Cyclin-K


Mass: 31700.471 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75909
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-RLC / (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol


Mass: 449.524 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H28FN7O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.58→216.333 Å / Num. obs: 72875 / % possible obs: 95 % / Redundancy: 21.1 % / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 3.58→3.83 Å / Num. unique obs: 3645 / CC1/2: 0.329

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Cootmodel building
STARANISOdata scaling
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.58→54.19 Å / SU ML: 0.3554 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2187 3658 5.02 %
Rwork0.1766 69148 -
obs0.1787 72806 78.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.28 Å2
Refinement stepCycle: LAST / Resolution: 3.58→54.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33662 0 229 0 33891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634578
X-RAY DIFFRACTIONf_angle_d0.973446768
X-RAY DIFFRACTIONf_chiral_restr0.05665168
X-RAY DIFFRACTIONf_plane_restr0.00695976
X-RAY DIFFRACTIONf_dihedral_angle_d12.477812956
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.14473197522
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.1697626348
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.939521688931
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.998367771483
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.686635553749
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.69854173594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.630.481640.32889X-RAY DIFFRACTION2.68
3.63-3.680.3387130.3224259X-RAY DIFFRACTION7.73
3.68-3.730.3007490.3084655X-RAY DIFFRACTION20.01
3.73-3.790.3892710.28971228X-RAY DIFFRACTION37
3.79-3.840.33011070.29931681X-RAY DIFFRACTION50.18
3.84-3.910.29471080.28292036X-RAY DIFFRACTION61.26
3.91-3.970.32271400.27672262X-RAY DIFFRACTION68.12
3.97-4.050.25721060.25652446X-RAY DIFFRACTION72.4
4.05-4.120.29241400.24622612X-RAY DIFFRACTION78.18
4.12-4.210.29541470.22862747X-RAY DIFFRACTION82.01
4.21-4.30.22831390.21252860X-RAY DIFFRACTION85.1
4.3-4.40.22741350.20043024X-RAY DIFFRACTION89.62
4.4-4.510.23711900.19133125X-RAY DIFFRACTION93.62
4.51-4.630.22961660.1863253X-RAY DIFFRACTION96.47
4.63-4.770.22371890.18443315X-RAY DIFFRACTION99.04
4.77-4.920.20921790.17553384X-RAY DIFFRACTION100
4.92-5.10.23771910.17613365X-RAY DIFFRACTION100
5.1-5.30.23141460.17393404X-RAY DIFFRACTION100
5.3-5.540.22981480.17753397X-RAY DIFFRACTION100
5.54-5.830.22321730.17913406X-RAY DIFFRACTION100
5.84-6.20.21551900.18813378X-RAY DIFFRACTION100
6.2-6.680.26931710.19143398X-RAY DIFFRACTION100
6.68-7.350.24422090.17873397X-RAY DIFFRACTION100
7.35-8.410.18681850.15843412X-RAY DIFFRACTION100
8.41-10.580.1611920.12323444X-RAY DIFFRACTION99.89
10.58-54.190.18371700.15313571X-RAY DIFFRACTION99.23
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)
11.934858631871.1607702196-0.4132827433070.7154975288910.1176743955131.13489955105-0.109830977737-0.325591796468-0.1739149738550.157810076061-0.0005664761675-0.05940162655830.1352647424970.223848846721-0.01807938057391.815943849790.174538556734-0.366711984251.54719713667-0.02161702699191.83540217352-57.7997611046-7.7657840435227.89354174
20.946532674525-0.0378235074901-0.0908959930082.424083243290.09894733463660.307484327714-0.167497175423-0.6552005756670.4274703400810.4053866362790.211247880553-0.536836214396-0.1945027683690.0571700380791-0.005067300182751.87522298201-0.024670330062-0.3079486937371.74689632844-0.1963041890541.5180257907-73.234782814710.009581258939.8657153165
31.877223277050.228110209409-0.8267206369682.93706249339-1.189682033851.455525698670.05749487805950.1142489534050.02899429814730.09326977339110.02305420655580.0741847760303-0.0663621988887-0.1833197728490.004493064885571.62463933687-0.052550373356-0.05339295672371.3101242351-0.1376732592561.42689311448-89.067680492718.68137652822.8324618346
41.927009472-1.2542805328-0.1822540017250.725164073425-0.3127583054061.316386736630.212164082191-0.06105839674190.3191468298560.253645177701-0.00680503642865-0.551769513542-0.2971524769930.3826436471920.04130203216461.80647870332-0.134770485934-0.1664238161421.47416439297-0.2076463196581.87553988735-60.435976742429.681717186121.7302862383
51.67293882851-0.0256651462274-0.5696493306021.00839643088-0.8299670866952.051756334410.2789791147040.308404436578-0.0437489191362-0.05632653684580.178135338330.149088380614-0.689976641273-0.197442699504-0.01830212126261.72949164266-0.0674007884839-0.08706306720521.54347787171-0.1492828271961.7804736076-62.165000031231.3740359835-14.81100017
63.052956160511.13092641085-0.3122842724462.11474226933-0.7846653025621.13428122028-0.168312406718-0.3349577254430.3738754828121.442990496560.4497498387940.691456335806-1.03978933165-0.405931370679-0.06973771475541.900495090270.09769221665230.0922216423651.78995197264-0.2297717492741.57237026232-62.228347988629.8631275837-8.65373456388
71.148542845830.055751424860.06232829535291.61331807899-0.5578353542791.7361100666-0.0516421177740.0396979040819-0.703115067771-0.184933049105-0.001180804674060.0510459702427-0.358395062383-0.552338510205-0.01469172244671.79382835836-0.0625461964948-0.02236400528961.65929069016-0.2828762492521.66058838491-57.187961462912.4174122697-12.2155985183
80.4635563192580.624777605656-0.05572819059351.27204838964-0.5951676320420.4458959967230.468850026222-0.173196084729-0.0791420258272-0.652399006756-0.349320503234-0.5006155780961.516466248231.66721105049-0.08017526228961.85259344969-0.1584090596580.01826306424582.10459274791-0.2350169381792.08114244678-41.052020635718.3060008393-15.7788372874
92.24487441192-0.342309816917-0.35064052252.22023548185-0.1063042018990.855497942227-0.04095042587480.02974779382240.370615607790.1507878585150.0716124178397-0.3259652782650.0358415185810.572167387984-0.0114216084751.586085753150.0275200282846-0.1182936857721.65106638659-0.274086600411.93564355199-41.21242447355.32255924339-5.46379241113
100.2706229703090.1427857445320.06460405107460.1655253154150.0621992745046-0.005002801147570.196213601867-0.1899728491910.315041991075-0.156643801458-0.404217301030.0904830421127-0.921249663633-0.520668036928-0.1653250855961.91864896216-0.133869493091-0.1640469834622.00761733269-0.3914047313072.53327708601-70.34826990336.74943827535-1.10363463447
112.04376698116-0.246346067230.7434358220814.21176326661-0.2256849870732.113184871880.1052844265780.6090232121590.8239214290240.5285203537090.08234800627351.13288234164-0.4313367659160.10818483391-0.08885216393381.58159359215-0.0158156210170.06628789058671.57365052367-0.03646412002771.26563072994-61.09806706840.4724887209-42.2424394648
121.31003665347-1.390289994341.199179401572.04726205818-1.336994251762.535037576190.2390373627460.6262680926550.780284278963-1.04511953503-0.0674550893285-1.15929285726-0.07396194278930.7174219636990.05223128079681.54329602127-0.3851890873410.003054937062691.62471834309-0.338002596812.07253040348-43.959211361443.5804921947-40.7359112827
131.581922054360.709884297822-0.8239101275521.2120577026-1.300398861842.13579299894-0.19972454194-0.3843863149230.266186040910.6577352179970.253291231111-0.341115025423-0.3817497506230.0148720643575-0.004926195187341.64304400973-0.120779460554-0.07515356669771.49304510365-0.2597642020281.81208419739-46.069072216943.1600258408-29.5121903487
140.325341491711-0.917082294031-0.1536380031111.759324395060.5179035262471.38959425708-0.103498339-0.429435196982-0.147403498879-0.003533922652470.0817228328419-0.670013649803-0.1705131685470.246379486261-0.01224328622781.62128259644-0.01355799101140.1813611254531.46619202956-0.1950169767291.86625584346-45.963707972124.1033289567-44.5738219261
151.41220246657-0.6465992491.007272378983.148392669890.5816757402081.01826608433-0.6165483788720.228616534528-0.112235117749-0.8020861460810.119967755579-0.4195831717740.317165707677-0.06504584876660.01226117849221.621573730690.0545807382196-0.07042559273871.41431122847-0.2570251327541.85866392399-49.819577894113.374641237-54.2216814953
160.202456172896-0.6388564468380.139925592593.50006757292-1.069536991780.868284568361-0.9504159820871.241253050111.89611025292-0.02611088576610.25876400123-2.60188929569-0.3559457979080.2056505421670.1258638638142.15243226306-0.0041664362603-0.371796290651.76156911990.1533909880152.46307491999-45.484092085933.0081502038-55.0254021061
172.57547722193-0.9689087156540.01648462049090.7718529058630.5002736739811.27037497565-0.1353882830130.3215575928310.134872928569-0.4225530581240.15891132062-0.222404659341-0.3134784542640.281296011442-0.02112506282271.87549015187-0.2837700906840.1423165791071.420025914190.02914329852981.30105215488-74.553084224466.9037120429-69.2482235309
182.10724287826-0.19360668287-0.1254481438152.123897510360.1622239396252.13334995549-0.0654302400427-0.4239991908870.0228455630739-0.4641960856210.0928549004838-0.0790119237457-0.10295719030.0679262767499-0.008612924708271.4158585897-0.0820736577123-0.04214996660811.44703767654-0.2039751797881.36716834237-75.838016275466.1846615877-34.3303438306
191.470981476670.4857052283150.3853582177131.54877724636-1.333049777053.33539895968-0.0157576147603-0.1249627665910.341237667179-0.0599714345877-0.05404056025320.189243106164-0.525170521215-0.414138572212-0.0526324209221.614335579230.0434629107507-0.1224312014181.36320697455-0.2336418859771.44511104406-97.092588118177.3324865692-41.6908466252
203.263292625751.091965327480.2695263506580.5656431264140.5316617330581.92865065811-0.306592044244-0.188564382414-0.1395626587920.3266781107910.5807648778160.311580003667-0.0206695056032-0.607782545296-0.03188436787671.70427376525-0.00638773466193-0.06652637235941.53086624656-0.04451027408571.54603727996-121.6643865253.7673618796-36.9628791238
213.640443558951.090249949191.688636878380.3265298561510.4054802513472.92519767417-0.627358619272-1.06767712821-0.8550782845190.4195435128381.033483446441.09294579456-0.7338373399440.475722151190.2172201798521.707425015870.0104483756885-0.1819412691521.49693419257-0.1098055648091.6870536598-126.37315337857.530414563-39.8019743443
220.80212262527-0.141252697859-1.235649581120.7929392162080.7024301883372.181182167670.219057216393-0.4863448626270.00637436733702-0.2528830160930.0142497725255-0.040823119618-0.7127928517980.0174450885482-0.007590242818691.69517340051-0.128897465646-0.1723762533951.53809720091-0.06100153436451.42008649688-125.73530340748.1683945979-48.4947427307
232.68627337177-0.4949117574670.5049190462782.092912249860.2697145358741.397196623270.122396491296-1.11865585806-0.371573590546-0.254724050016-0.1531236951820.0567823217903-0.6816617809320.853961297801-0.05263616391061.55443470017-0.0566871585974-0.212554304391.78646021896-0.2108172683811.50843467244-119.14487659156.5668748302-42.4518448537
244.03463789541-0.847719084928-1.384122197321.82748871348-0.5377097091771.510525169940.4036002393350.594438119856-0.3710202217430.3025775911370.338401046527-0.5433382083250.5378861982370.041739452025-0.02277811166611.63715411245-0.0421937651885-0.1458328449621.64664120953-0.3793146744281.37849951546-112.0532056244.1478466827-62.0032219
252.732709469460.3994172216010.01191148561951.343377519090.2588921897761.553820139090.130642457607-0.1380636031660.7280419965950.558834969352-0.04562746703010.0445257975951-0.09136657872090.594083641856-0.002613546572531.58570642678-0.00937885136342-0.28625655211.55890535908-0.1408530538451.3935625392-117.58797225451.4188836544-55.8752660876
260.653171034763-0.416834934927-0.5042924653041.18741381573-0.33921694640.798428886464-0.01458221720990.692082992102-0.5048570923620.691618465603-0.2133111573370.683263051673-0.0109074327032-1.022763143050.09935964757571.976855971550.251160713039-0.3683119156771.94852813347-0.05644385439562.24037301409-129.23838516656.4860219255-65.7003965658
270.0825801787958-0.3693454991590.05247934249231.7077070223-0.02382508085791.618998573180.958007028662-0.5677803354670.6888060381980.206083336702-0.30413215613-0.209068177459-0.806449304836-0.7332190011450.007711837898932.009691386840.0942776988621-0.266906975971.433576288430.1169983880411.559520394-118.63426891856.7773800714-69.0327006987
281.749526457830.4289868860850.279775971711.539201324410.4969093967161.634423772880.1718149819231.119906952330.545951606943-1.4912417483-0.0276287727249-0.231128156251-1.27854157922-0.3791391373760.02004091184962.764648060570.301007094911-0.3320239283361.74620445723-0.05463722506271.43079725855-116.91808913464.6544649041-78.03560074
294.39497474350.402848302726-0.2231328030643.016785827521.159981667081.506168608850.008342381070060.226608166421-0.817544427565-1.252160740060.309591307250.1150844747440.718878421080.2140759105250.01419292213541.730427106090.0283951235829-0.226732854321.3832656582-0.225085651531.38022241279-109.29714174447.5293009886-73.2163586927
300.424343947050.357833247574-0.5776599336910.265178052465-0.4997625820990.893220716138-0.861139065967-0.478976010020.9823245641050.634735087990.236703451491-0.658409137896-0.2145809220630.539974539634-0.2207758906512.24150333840.461759067542-0.2934393032072.75857052890.002618040829112.93282758469-94.665527719151.5218195297-49.3012654615
313.32045016591-0.302506745085-2.309331822152.485138172930.5914231109533.9606193486-0.211176079734-0.400878884284-0.3393407414920.6615099414360.1905832801120.1125155091360.193556726983-0.0409095177650.05396817683941.43255942701-0.091019600722-0.06562416639631.555364320180.09903240195261.39921214659-147.51898391336.8750568955-35.693725261
321.961449165270.585650742468-0.3461511634151.55304094059-0.4119338419161.44366212018-0.1880574015340.302848729448-0.421821691119-0.0406890596922-0.004836812828520.6949678407020.0761997254004-0.623111810117-0.0273297032491.279818521930.10202994953-0.1865784590621.242943270980.006113257776791.48752843438-151.06174612149.1287884215-44.6252218583
331.80803908611-0.1238445125880.4802308938281.77348585082-0.2624179177431.19000135749-0.177797347652-0.3344907023281.30478222126-0.1361374142080.201913045321-0.738370079263-1.35455992759-0.376735537169-0.03203902191891.706246517740.177041006709-0.132129618651.47481763713-0.06336084866491.50337501623-149.77282874259.9639414683-43.6777105036
340.8707510493960.88138604361-0.3429370206991.218243948920.8043925614652.017033987550.001993599520970.5279124354620.0794408809390.05558888458540.0581434488873-0.3918866296660.4923797441210.117292533206-0.03393029128341.450593344610.0426797902111-0.1150151710011.42008596849-0.01523519246211.47933021137-149.14112943135.0018058164-58.2090484879
353.34199853756-2.166952601980.6987831940612.432638615940.2610276173220.765237067152-0.1188042674410.0773151474208-1.64117276162-0.6103497135540.3375648658720.6699225526960.425731751162-0.131368210092-0.07442282139471.828907338380.1498945603560.01251393741521.28081402151-0.1756967817811.31975749431-149.85580850719.761401749-66.8453444308
363.089051666511.05215217097-1.102186610674.16639648496-1.687113680745.298569451540.211652925369-0.668421515623-0.2951867192080.1526935258161.16209807242-1.148072068340.1564047427850.4598523555720.03489272939531.766557539490.284577707429-0.05224098324641.376143855250.1759616743231.51426225052-143.64520832222.8513714927-58.0094640174
372.500015767060.136284992371-2.375338785082.586622874582.265045328584.468657822660.933492577051-0.881279225199-0.3628688307311.03751003214-0.534262042791.42844948318-0.0821250757718-2.13012441056-0.07914807371341.5493909343-0.1138319689950.0385300922532.133437286630.07163680022941.76341042102-160.61301926431.5248188204-51.8048198615
380.79834240177-0.182107314270.3715081393590.766270234179-0.1687909803653.16540896579-0.0459245268699-0.0981866594626-0.01204300774510.01129246410630.06759745367920.720600900295-0.242290616412-0.518454985097-0.01697905077931.613847438910.1090334559280.02259360292311.556082681470.1406761989841.99288346869-173.0569133320.1145427682-8.37635209304
391.92372703888-0.471811912948-0.05445940048891.58693151578-1.564099459361.54404940701-0.254383920621-0.1880301330840.5181146592960.366691726310.2795242139110.637136860102-0.742133038779-0.2560550995040.04637266175472.00376536340.156445079275-0.0613941879691.300087114510.0129747610551.81813139776-157.13427418945.8945066417-5.25327873504
402.014244237371.36646049880.8897643648541.3272493380.1686765491262.108877298670.06537978120830.5821524804730.3191910913070.02233679790920.329068994994-0.526380091577-0.239390236570.517762782688-0.09771500019251.83474017965-0.01632275000470.01427309224121.318648840950.06430719458471.73998723256-140.21317104444.4083651241-11.822734348
412.359782332130.585941443836-0.4072445477531.28112192479-0.5962983104851.01991125718-0.0104241154133-0.6896440509880.1628965451170.7573908329870.03468418851880.0749428181944-0.388136004036-0.0527245893593-0.05016870758732.081240763860.1305430871610.03661174712891.40727058124-0.02857740324141.45508517124-147.00026883733.915830729415.5400522221
421.23098106123-0.8959717529321.236419054692.81575900788-1.210380298521.277525139130.167266375509-0.1227342701860.3511350220450.1004509202170.09824371599-0.369886452306-0.4883696427010.7298680908610.02105529726891.829796790440.0921502480768-0.008304687706461.520829396990.03534667098551.69304587708-119.34992743713.522425819913.3674196048
432.723939216181.15879603560.1593143653011.19634759458-0.332574135480.793339993153-0.09084981986840.05633017016960.176277213196-0.03568638468650.0038363889032-0.536573652444-0.4729171376940.1485707797520.08072825906881.700213949930.0433022737278-0.004316060470771.32920190043-0.1138841557931.57770689205-123.6037961643.5903116151617.381738996
441.009900742950.01798419656050.8450180789941.79149509607-0.3321774873522.38436698275-0.0740045885593-0.01620043953120.869424981246-0.397625215991-0.455686932255-0.8496161520050.2153532868430.1490447196660.1916913188921.594527315460.1539165584670.1337443734981.34031206940.1411968509981.86905011442-126.7700389812.14813761914.6404590268
451.989000805140.309160531459-0.1644738472111.625220276020.2392721568022.4168116322-0.007029283170370.283860972804-0.256807766213-0.4575964090390.06891978388920.403985539407-0.1628919545040.468851529579-0.01466691283791.61512356408-0.04185816673130.16306898621.22130638548-0.02829938650581.05401147731-136.039336985-1.272114928813.8376132766
462.850290166710.623434894792-0.09326603996941.6182014711.636887383712.7941721213-0.442318219168-0.232532947196-0.427808610090.5833029635430.33376443184-0.1583019118440.203510200779-0.8695203401460.0585724695761.88859139336-0.150928568998-0.1109571240721.217578479490.05289928502171.62248796106-132.698387586-9.1834283889615.9294506179
470.9324265900140.910016837094-0.4735146086342.49682997715-0.2825998326651.37488120676-0.148809610746-0.7354016686150.3679805764871.02707689273-0.002514946663140.282539197843-1.233669831260.1104130493420.04108551954361.522722012990.02895971589240.1210355436391.325331334160.01520210040671.38322431639-144.949919026-5.3811455576315.143360327
481.44205647207-0.2359821990660.201955049892.17200433122-0.8974095179221.185496431060.0308454499012-0.579499165756-0.5400489402620.632651727640.008966702209450.813177116564-0.323771466406-0.129472809621-0.05046371688631.68596109832-0.03855445273750.2589225370241.46410213102-0.003172602172161.6276196068-157.134597434-8.089422452416.6142251368
492.51980786158-2.071915581191.129159644923.06599103351-0.148352222543.09849203275-0.1811490694090.394255485362-0.855730438204-0.07584138733430.09991735677110.3009410390590.0570445009607-0.0885384747464-0.07068823432341.54288358303-0.02069153333740.05078425939321.195506071450.1198021444671.36067570842-148.326556145-8.40852758976-0.42615383069
500.796929359222-0.4624708483450.3760864876060.295857072255-0.2759756764110.6627218371620.135554565857-0.5527954968650.927936712261-0.04156626017890.2976049798531.54228072925-1.45674886101-0.0309856361711-0.03816488114492.986744801070.0176503992521-0.1542682406541.773468463060.1485634746152.26653829971-143.14751887221.0408516723-6.4821761256
513.89010475451.129964352621.309979416931.809977126421.02655863493.73685125905-0.2017033382010.4495710544-0.242009457567-0.258083623169-0.0143766683714-0.2333997483650.08461108070570.293725506646-0.0124251215841.611054206870.0655565615575-0.1576834226531.42867945642-0.0752667963191.5490587169-98.6999461196-7.9401339483421.4057879958
524.259294769110.1936065849010.3365911936160.9332737513080.4470492050530.417156992998-0.502979166968-0.406350582924-2.173578103470.2906496779480.2860043525190.537258287360.5356056506680.7094238220830.02408212524172.264711961220.1477838544790.0009888443827761.212640116870.05315297306441.49618305542-106.566732713-14.467607569735.6949428211
532.45512129281-0.5970712825030.4391411153391.51538360547-0.5028140038021.594856367230.13896862685-0.5740430219590.5229087826970.137005319582-0.4375532519980.143442738659-0.479822116662-0.026456909224-0.01918522700581.733964492510.03725860995130.06040963422181.43932306513-0.1032080018431.14480480096-113.618215404-5.5569566547534.391664448
540.7709974617730.01696135890310.1506256748491.867764487330.9851543340950.745515642774-0.2337319299060.2898846097870.105813161833-0.0764013462024-0.1564691062780.6946916240150.375669028609-0.311517695087-0.02135661565571.66578038741-0.04427359192170.1677257670351.15518221138-0.04065289666221.47112077574-113.017076642-25.130614213620.2011784134
552.410952207270.7283802169870.1641633900431.551937227821.493007272142.104333772840.08433013095790.437664234499-0.270694065768-0.5593051075740.1032493745730.6027936589170.802750708350.3171376288490.006476752087231.952251053660.002773974352630.2007216216321.49315871415-0.1598509064321.3668348196-110.049126434-34.99675766429.38534823224
563.7863321270.6359485663082.784964827921.960216151660.8194926107172.15102466399-0.217266041348-0.996305095433-0.8864171180551.11546044102-0.0414968053672-1.438104287410.9891281532041.341170496520.00205566901122.066639219610.383744039922-0.004945477554691.594453241770.1171190043371.658643306-101.042315284-28.959441857726.4380701646
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 307 )AA1 - 3071 - 307
22chain 'A' and (resid 308 through 716 )AA308 - 716308 - 402
33chain 'A' and (resid 717 through 856 )AA717 - 856403 - 542
44chain 'A' and (resid 857 through 1140 )AA857 - 1140543 - 826
55chain 'B' and (resid 715 through 794 )BB715 - 7941 - 80
66chain 'B' and (resid 795 through 832 )BB795 - 83281 - 118
77chain 'B' and (resid 833 through 880 )BB833 - 880119 - 166
88chain 'B' and (resid 881 through 901 )BB881 - 901167 - 187
99chain 'B' and (resid 902 through 1020 )BB902 - 1020188 - 306
1010chain 'B' and (resid 1021 through 1040 )BB1021 - 1040307 - 326
1111chain 'C' and (resid 20 through 42 )CD20 - 421 - 23
1212chain 'C' and (resid 43 through 63 )CD43 - 6324 - 44
1313chain 'C' and (resid 64 through 150 )CD64 - 15045 - 131
1414chain 'C' and (resid 151 through 217 )CD151 - 217132 - 198
1515chain 'C' and (resid 218 through 243 )CD218 - 243199 - 224
1616chain 'C' and (resid 244 through 267 )CD244 - 267225 - 248
1717chain 'D' and (resid 1 through 361 )DE1 - 3611 - 361
1818chain 'D' and (resid 362 through 819 )DE362 - 819362 - 506
1919chain 'D' and (resid 820 through 1140 )DE820 - 1140507 - 827
2020chain 'E' and (resid 715 through 746 )EF715 - 7461 - 32
2121chain 'E' and (resid 747 through 768 )EF747 - 76833 - 54
2222chain 'E' and (resid 769 through 794 )EF769 - 79455 - 80
2323chain 'E' and (resid 795 through 832 )EF795 - 83281 - 118
2424chain 'E' and (resid 833 through 852 )EF833 - 852119 - 138
2525chain 'E' and (resid 853 through 880 )EF853 - 880139 - 166
2626chain 'E' and (resid 881 through 901 )EF881 - 901167 - 187
2727chain 'E' and (resid 902 through 931 )EF902 - 931188 - 217
2828chain 'E' and (resid 932 through 980 )EF932 - 980218 - 266
2929chain 'E' and (resid 981 through 1026 )EF981 - 1026267 - 312
3030chain 'E' and (resid 1027 through 1040 )EF1027 - 1040313 - 326
3131chain 'F' and (resid 20 through 42 )FH20 - 421 - 23
3232chain 'F' and (resid 43 through 106 )FH43 - 10624 - 87
3333chain 'F' and (resid 107 through 150 )FH107 - 15088 - 131
3434chain 'F' and (resid 151 through 218 )FH151 - 218132 - 199
3535chain 'F' and (resid 219 through 233 )FH219 - 233200 - 214
3636chain 'F' and (resid 234 through 243 )FH234 - 243215 - 224
3737chain 'F' and (resid 244 through 267 )FH244 - 267225 - 248
3838chain 'G' and (resid 1 through 325 )GI1 - 3251 - 325
3939chain 'G' and (resid 326 through 755 )GI326 - 755326 - 441
4040chain 'G' and (resid 756 through 819 )GI756 - 819442 - 505
4141chain 'G' and (resid 820 through 1140 )GI820 - 1140506 - 826
4242chain 'H' and (resid 715 through 751 )HJ715 - 7511 - 37
4343chain 'H' and (resid 752 through 794 )HJ752 - 79438 - 80
4444chain 'H' and (resid 795 through 832 )HJ795 - 83281 - 118
4545chain 'H' and (resid 833 through 872 )HJ833 - 872119 - 158
4646chain 'H' and (resid 873 through 890 )HJ873 - 890159 - 176
4747chain 'H' and (resid 891 through 931 )HJ891 - 931177 - 217
4848chain 'H' and (resid 932 through 980 )HJ932 - 980218 - 266
4949chain 'H' and (resid 981 through 1026 )HJ981 - 1026267 - 312
5050chain 'H' and (resid 1027 through 1044 )HJ1027 - 1044313 - 330
5151chain 'I' and (resid 20 through 42 )IL20 - 421 - 23
5252chain 'I' and (resid 43 through 63 )IL43 - 6324 - 44
5353chain 'I' and (resid 64 through 150 )IL64 - 15045 - 131
5454chain 'I' and (resid 151 through 217 )IL151 - 217132 - 198
5555chain 'I' and (resid 218 through 243 )IL218 - 243199 - 224
5656chain 'I' and (resid 244 through 267 )IL244 - 267225 - 248

+
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