[English] 日本語
Yorodumi
- PDB-8bur: Structure of DDB1 bound to DS50-engaged CDK12-cyclin K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bur
TitleStructure of DDB1 bound to DS50-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


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / 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 ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / 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 / nucleus / cytoplasm
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 / 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-RQU / Cyclin-K / DNA damage-binding protein 1 / Cyclin-dependent kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å
AuthorsKozicka, Z. / Kempf, G. / Focht, V. / 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 1.1Mar 27, 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
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: 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)500,51536
Polymers496,5589
Non-polymers3,95727
Water00
1
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,74211
Polymers165,5193
Non-polymers1,2238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,03114
Polymers165,5193
Non-polymers1,51111
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)166,74211
Polymers165,5193
Non-polymers1,2238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.266, 250.266, 217.643
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_2(chain "B" and resid 715 through 1039)
d_2ens_2(chain "E" and resid 715 through 1039)
d_3ens_2(chain "H" and resid 715 through 1039)
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METGLYE1 - 393
d_12ens_1LYSHISE396 - 827
d_21ens_1METGLYA1 - 393
d_22ens_1LYSHISA395 - 826
d_31ens_1METGLYI1 - 393
d_32ens_1LYSHISI395 - 826
d_11ens_2THRCYSF1 - 325
d_21ens_2THRCYSB1 - 325
d_31ens_2THRCYSJ1 - 325
d_11ens_3THRHISH1 - 248
d_21ens_3THRHISD1 - 248
d_31ens_3THRHISL1 - 248

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.473378900922, 0.505277517258, -0.721531043487), (-0.510960117135, 0.509717549664, 0.692176117951), (0.717518065877, 0.696335156457, 0.016887125963)-179.063880818, -30.5305707552, 37.8470451082
2given(-0.503189922858, -0.499102316937, 0.705476277959), (0.553650421585, 0.440624858074, 0.706626453741), (-0.663529285121, 0.746154549457, 0.0546102198425)-127.596667669, 83.623880856, -104.451181386
3given(-0.512266388454, 0.494826991888, -0.70194686078), (-0.51643988825, 0.475564533793, 0.712129353434), (0.686201857389, 0.727313290335, 0.0119326701906)-181.296781855, -28.0760945057, 32.5720126034
4given(-0.468446100279, -0.524962889057, 0.710613971328), (0.543058322248, 0.46334481501, 0.700285114108), (-0.696882995754, 0.713950661823, 0.0680333940977)-122.440366765, 80.7973910212, -105.70220367
5given(-0.559777007111, 0.474588038463, -0.679276008746), (-0.51203216144, 0.446415069033, 0.733850565027), (0.651515746518, 0.75860383593, -0.00688855214462)-185.36281672, -25.1013006425, 25.4820000941
6given(-0.445287357922, -0.525365820093, 0.725058565878), (0.520866044845, 0.506670966374, 0.687010258411), (-0.728297832073, 0.683575370323, 0.0480310408565)-118.911162916, 74.7803023239, -109.119448351

-
Components

#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: 93675.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: 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.: 24 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-RQU / ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide


Mass: 550.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H34N8O2 / 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: 1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0

-
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: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.64→216.737 Å / Num. obs: 79836 / % possible obs: 96.1 % / Redundancy: 21.4 % / CC1/2: 0.993 / Net I/σ(I): 7.9
Reflection shellResolution: 3.643→3.812 Å / Num. unique obs: 3990 / CC1/2: 0.273

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Cootmodel building
STARANISOdata scaling
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.64→97.25 Å / SU ML: 0.4417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 3981 4.99 %
Rwork0.1894 75796 -
obs0.1916 79777 90.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 144.55 Å2
Refinement stepCycle: LAST / Resolution: 3.64→97.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33652 0 243 0 33895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005834721
X-RAY DIFFRACTIONf_angle_d0.928846957
X-RAY DIFFRACTIONf_chiral_restr0.05465167
X-RAY DIFFRACTIONf_plane_restr0.00655995
X-RAY DIFFRACTIONf_dihedral_angle_d12.191113106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EX-RAY DIFFRACTIONTorsion NCS1.08842578136
ens_1d_3EX-RAY DIFFRACTIONTorsion NCS0.905314902863
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS1.05654097605
ens_2d_3FX-RAY DIFFRACTIONTorsion NCS1.05039917175
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.735324108286
ens_3d_3HX-RAY DIFFRACTIONTorsion NCS0.652086811846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.64-3.690.424380.3145246X-RAY DIFFRACTION8.16
3.69-3.730.3626470.3112818X-RAY DIFFRACTION28.11
3.73-3.780.3618900.30761527X-RAY DIFFRACTION52.16
3.78-3.840.34191220.29262232X-RAY DIFFRACTION75.81
3.84-3.890.29861500.2942592X-RAY DIFFRACTION87.55
3.89-3.950.35531460.3012786X-RAY DIFFRACTION93.91
3.95-4.010.3091520.27312827X-RAY DIFFRACTION95.82
4.01-4.080.30221370.24752882X-RAY DIFFRACTION97.32
4.08-4.150.28461630.23972960X-RAY DIFFRACTION99.24
4.15-4.220.25311480.22322949X-RAY DIFFRACTION99.84
4.22-4.30.24631450.2072970X-RAY DIFFRACTION100
4.3-4.390.23551380.20222973X-RAY DIFFRACTION99.97
4.39-4.490.26191770.18992971X-RAY DIFFRACTION100
4.49-4.590.21371550.17732949X-RAY DIFFRACTION100
4.59-4.710.21671520.17362982X-RAY DIFFRACTION100
4.71-4.830.22141710.16962966X-RAY DIFFRACTION100
4.83-4.970.1851600.16772960X-RAY DIFFRACTION100
4.97-5.130.24181760.17642955X-RAY DIFFRACTION99.97
5.14-5.320.22331120.17853038X-RAY DIFFRACTION100
5.32-5.530.23231340.18313018X-RAY DIFFRACTION100
5.53-5.780.25411490.18482990X-RAY DIFFRACTION100
5.78-6.090.22731560.19362985X-RAY DIFFRACTION100
6.09-6.470.27361770.20022991X-RAY DIFFRACTION100
6.47-6.970.26541630.19672995X-RAY DIFFRACTION100
6.97-7.670.23421780.17913005X-RAY DIFFRACTION100
7.67-8.780.20511670.16073024X-RAY DIFFRACTION100
8.78-11.060.16251680.12253057X-RAY DIFFRACTION99.88
11.06-97.250.19151400.17893148X-RAY DIFFRACTION98.56
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)
11.434142661141.10384061071-0.04188492022550.640702939656-0.1937434586071.1736969856-0.0766064250086-0.310733523606-0.07050608685390.270377466590.0370884272346-0.1952730389640.3551905584020.4210333339538.90276988048E-61.372668997350.275571008354-0.31389941691.19971787034-0.07974499759241.34327180533-57.3361883757-7.4903643058427.989592801
20.237832163702-0.206781718375-1.451430764180.1385743602580.1516094728730.519358184422-0.00718240512309-0.598448651333-0.1380023706180.6035671998610.376856427336-0.388255418788-0.03326067227520.3188276213376.14551985032E-61.431074753370.0704128519012-0.3096505778621.22829854787-0.1843728968821.24490646436-72.846551161810.190413563139.9725232306
31.73925177415-0.295666473977-0.863121611251.79813042344-1.205613503561.449145382880.1131163409890.0388885702896-0.01714160994010.0653990978090.0315480531453-0.00702328060628-0.0562861966279-0.16688089215-2.27218533895E-51.170228736960.0525780207673-0.0397284880940.882932867315-0.08187738331830.953343294044-88.955999048216.012310784824.8946723846
41.49699340694-0.414227208252-0.4163202999220.353750682663-0.2814983610860.6929745941190.1929257787510.109846516740.3013707090480.0765028853391-0.030964764653-0.293695482721-0.2335524493290.301879833854-1.99291399794E-51.19852045937-0.0619539327144-0.1316148202411.00749272114-0.2092087332371.24280766772-63.464597631829.571237740821.393733985
50.3308093389890.6295094034870.554683900634-0.0176499712712-0.1030825155931.213990176240.2071843540170.02452833936510.09805082099430.2395934790220.1465755185840.246130393826-0.2228106607220.159378985414-1.166694524E-51.32315858293-0.0263567488455-0.05981538748731.27024023858-0.1372731696721.25723360175-61.863751086331.6858207254-14.7761836319
60.5357232864040.2707190795470.2904328300992.14009021033-1.637843007581.048310070980.05430753802090.0604888051277-0.250997642248-0.1140386180830.02492159924580.547737159748-0.09188715526780.1225486298928.49838554898E-51.364626504570.01011044605550.0472782553671.21442788692-0.1906958034641.29510980401-57.072743080520.0528718703-12.0925890911
71.356200908590.1531927982660.3028488322762.374320615180.9223453804541.66630515603-0.2034413062890.628849221415-0.0951715746578-0.2103505510490.168222535443-0.170292694798-0.04637063088080.3903533340672.77084395366E-51.16798801072-0.00128721688295-0.1544465731481.32740433128-0.3152139278471.54818309666-44.89441709736.79847602607-5.21427892211
80.181913246310.0554569131487-0.114185405952-0.0404152754194-0.20889663666-0.02680174880860.2439639835990.3474317285820.3812568212740.6158386897020.01905713216190.4783761400150.130758645653-0.108909918087-0.000235457516931.44550967074-0.02470020802110.1960853840511.26805571248-0.1148421224091.29880477251-61.103078025640.6927835434-42.353717483
90.280744723797-0.0735492026245-0.2652090217160.017712549256-0.0495100545720.2546407210410.2172716995320.0301283422371.33458018156-0.427536734741-0.126398689345-0.37036507784-0.4233370146540.1987558207190.0001108062825981.06499103926-0.1651119886740.03910574068281.36461504361-0.403260712451.52096772251-43.898297752243.8809658058-41.0144495962
100.9182718903811.00228671561-1.260020148821.05411012015-1.443466208721.658029448910.126688604799-0.336665797820.4101947171140.5994792116580.0848949242442-0.361355634316-0.10702532941-0.0337401422851-8.74431353498E-61.18157538943-0.0792418106739-0.07948790871131.17893111395-0.3538815082411.40112675911-45.970542325643.4624753521-29.6815622453
11-0.0313398050131-0.2384132737180.2671158755611.22928681998-1.111133964530.8240081487780.00418608647394-0.288979872905-0.593364964093-0.19963090338-0.0423437642862-0.446041577509-0.2257451233750.292401360248-6.47658345183E-51.182653670360.01174412401630.1421425749011.04838182163-0.2055417813821.61104710599-45.655015029924.3874776513-44.9606680218
120.0858854715845-0.009715479005750.2933356541940.1136470192040.1199232655920.271591051345-0.6264849391730.08482326272220.364505712943-0.6446617379210.623932709617-0.5490594567560.262218052662-0.474836153425-2.77789228106E-51.35193909731-0.0520785630786-0.08799268803041.23156742175-0.2786082350981.6120722001-50.010187467413.3387417503-54.1491156046
130.176996612948-0.0823082421090.05704880767190.01962710003280.00829369046513-0.101782965191-1.106268320991.304711530351.2580597332-0.5395692814550.363274828408-1.00692971345-0.592155746972-0.6323878414560.0008887923871511.51394031948-0.0961104980389-0.1800454589191.26364265369-0.0006223366900921.42617497551-45.303266892833.0816701612-55.4817122708
141.93301079406-0.573232309920.3993156500520.9808576662980.1165749824180.81766377664-0.2141603433290.2751875663310.0972673354793-0.3679758256020.19596085588-0.134545783758-0.2668257422550.3302312984218.1789801978E-71.39766238778-0.3068494905070.1295432990430.987185598132-0.0188020751850.901932381527-74.666747371167.0952206785-69.9680202372
151.312920137390.494105970551-0.8524481835960.760448076531-0.1115002716990.512930953864-0.230124037738-0.3887621067370.270542309949-0.3420671996560.239877388049-0.418830481924-0.2781211435380.2200852341615.16117226277E-51.17019615983-0.0779401462733-0.0811946915821.01988871152-0.1625262822711.14272902215-74.99163238472.2899114377-37.0787286837
161.49838200920.0366556030597-0.1021559230341.22115669412-1.178855789361.722368129740.0953625562714-0.340159746232-0.171333859396-0.1378488412590.0193887161754-0.3785503292840.3823690574820.179155797843-2.40623829865E-50.999602223499-0.189385583008-0.08355512881771.05551356714-0.1366431118010.89049444205-81.04488133759.0292742497-29.5072097039
170.667510437096-0.04826125124720.2651624465231.43718809437-1.069047555152.23215613886-0.083938756716-0.1854627681780.192357841519-0.1328439623930.1147111604590.279418492821-0.440117838455-0.617862129148-4.49776307814E-51.239702097430.0148807820113-0.1393684881161.04280237266-0.1949660032951.07725563231-98.623116742379.7442891907-44.0783518631
180.5294539001970.5960758215790.8372493977180.3517179919980.2402924211760.65312175319-0.497784969297-0.3756164606360.1125846930510.2596983725510.5025855378950.0576968905599-0.04316770303590.00331202396691-4.61356206548E-51.138918890820.13409123368-0.1341730711641.18002803199-0.05035287250161.28651349237-123.85859435755.5370871779-38.3461627454
190.163535805986-0.0527660731319-0.2703156233390.296740029349-0.4058186483440.3728094352830.3573791058830.56033496338-1.28613382475-0.218686457845-1.075031894640.373118774456-0.295730375265-0.899478071180.0002535288793271.1986922241-0.03503056839940.03322967416561.23135057986-0.02456147367941.06828154777-126.03095402148.0768507833-51.6865023087
20-0.01097484418190.139861237518-0.09190876852420.75907558498-0.5585323351780.228864284602-0.542630871975-1.84717714204-0.4368931127240.3846636578190.52174057179-0.1389952583180.544733855190.664566003460.0002050203945660.9897347170820.0233854654308-0.1947653946521.47129941131-0.05730478822641.32231587256-130.99905233155.7338192556-34.9466747363
211.09325267556-0.621282285519-0.779644799231.00110318064-0.2997789253711.87096483975-0.231363622670.177346669871-0.09349497883670.3789534292070.392972427538-0.13446564848-0.4558072222110.381627030634-3.50288139726E-61.315682529990.0230497045083-0.2311602979861.25645978541-0.1405419648051.15377934731-112.44488153550.3791615055-57.3441343858
220.007669549825860.135166363181-0.05973917862620.0006048477647270.0208522514130.005996863358080.132936014505-0.0842332418303-1.40494461074-0.531473618965-0.0603253971497-0.8428254107340.156411806092-1.068850441352.14288103401E-51.512251506010.126159832115-0.4057492701051.52955834854-0.03063007871951.8797856823-129.44354561456.4661972871-66.1333257722
230.364074198705-0.171369704267-0.174746518649-0.18707375666-0.07690292587910.2624026829311.180347286290.4905775981510.00629528401341-0.758005783469-0.344980763199-0.0282838277665-0.84349760442-0.05653982721972.57838468322E-51.540002155890.145053168926-0.194135540721.148064900310.04323288475230.97315637407-118.94723370356.9377309713-69.4343284126
240.5619210292520.273016804549-0.3230665338090.982858734349-0.3693750483230.7416828600280.5082367443340.9065194011940.470688154395-1.11324336566-0.1662269981880.258017683621-0.940492355353-0.4292296350770.00013417013742.290407118310.261425710534-0.3159822725671.27314141563-0.06144238299191.33373694225-117.33051551964.7559714272-78.4150016791
250.5267171292610.153425849152-0.1654533325040.7226361694250.4839955228580.304136437607-0.05319683398190.0196340569345-0.0331685704971-0.6952767145970.07609829653020.01356295490950.1386745835590.117162268785-2.28445119704E-51.39937614454-0.0425694536375-0.294774765971.0361696487-0.02228394348671.11354751784-109.59443479347.6303445663-73.5617057686
26-0.02835420068570.01380306822650.119791340830.00431081821553-0.163192035790.190884371548-0.0140023141128-0.3213094345231.91012890881.199953489510.1767945449840.02922862179170.453476366106-0.0836100118734-0.000576137610211.434749016680.1632074442730.1564431512671.74990154816-0.2747872942362.10324107729-92.204920534654.3493004124-49.8567175098
270.6062165457060.1541519315710.3066619492950.319472877069-0.3274971062940.4710763258330.374650096312-0.707965769837-0.4459156228690.7354862618360.281535243816-0.435163637618-0.0452065189830.2109366557320.0001942393293121.15383065959-0.0868781594654-0.004686191741921.2311863480.01161767905431.21991255128-147.4694319636.8942862928-35.6746027104
281.485953666960.0531617057758-0.4641439235252.571570966820.1854073698311.04788361591-0.1427360932440.301877079795-0.4084479734010.1191625819790.1661863813710.2431344789290.166431139457-0.480952659571-0.0001275851761990.970081070790.0611306920369-0.1616701433190.9421060953970.009374039902171.00500484872-151.3159336349.0993913-44.5605872711
290.4696432735260.01472906925430.8303481683272.28929499841-0.52236099941.5266782013-0.3605424294160.005742027512470.988283537937-0.1031788702880.241322985465-0.218154482557-0.600672709182-0.285999752816-0.0001130305972421.131250687380.107272123841-0.09219010207311.04724541589-0.05466274036790.979824391614-150.14349280759.9372485631-43.6423693951
300.638330244498-0.897223426346-0.1829025331541.339057917770.720833107971.068335229670.1621293564520.261943137844-0.3019361003760.265312439643-0.07677120160210.00285300165570.3820884534170.113319132445-1.36625709274E-50.899036081195-0.0426810572787-0.04230841432790.987576829513-0.01385519850560.925154804389-149.30421254734.9479266661-58.1383903289
310.205532209655-0.1146632221650.119066137980.4731473393010.2045612238020.05390100896820.0266115520380.23214722997-0.442512935335-0.1633270610240.0571469522938-0.148075578405-0.3144380509750.2304997319210.000106637063741.226168317080.24022868499-0.0220570755511.03593636813-0.07405373839121.11166147541-147.48387887420.8941945202-63.2771531774
320.0199494639002-0.0879796590491-0.0200483290202-0.0676178590387-0.0124793718021-0.04852548213540.322057930783-1.10032437833-0.8459381319350.5878271901220.1304555827280.7075227204710.0941668963995-1.033399100620.0001502548591021.022575785250.01994564366520.1561557343651.26183461231-0.1535630421761.10483390819-160.87807572631.117007003-51.6447427554
330.919107889159-0.354228601034-0.2067992625981.92803767358-0.1068970157082.84810569607-0.1445259427930.128641893789-0.283334422483-0.1462552139860.3142206958440.9690643370620.00716184706817-0.190326233326-4.56905626277E-61.082553651160.0601545838429-0.05076600323551.084948123220.190001028141.44294505311-173.08232123119.1228490364-7.26639379212
340.7986437450780.964286555042-0.3563259371781.963896631380.007459911612920.20233955897-0.3828684668910.3604605018610.6857678991980.242623222090.3195395600840.637761034156-0.514292095058-0.04613405076541.95332241624E-61.486190592020.265518260401-0.1391346239020.8858233199340.05198355118811.22888612466-161.61854616443.3905418683-6.78384507112
35-0.043364096378-0.06533719493790.2450985542150.205710073303-0.07989057507550.222662023046-0.1875568318620.2978839863230.1828791795250.0851531056911-0.227751929277-0.116026626204-0.04771554510950.341512442314-8.67313402388E-61.36772563785-0.0376752643496-0.129772383021.120173250530.01489867475141.10438275716-140.96231950642.2136182462-17.2827833912
361.089294098380.123335850720.1321308329331.20220039274-1.220393038070.865154636742-0.2397385280050.298042319980.0778739594108-0.4521873748040.0650068191846-0.677925969684-0.4276989412790.0359465229441-1.13836051285E-51.424358591420.00379081145847-0.1245934231980.7226012034850.0008320181636541.31509634612-136.75742473245.7425926297-4.38241611549
371.741437341060.287530039311-0.3110655340721.99427482049-0.8586890418710.331958824301-0.210341677301-0.5673896887580.1292709725180.9416610795870.123125762011-0.303772335279-0.525863606568-0.10232371987-9.52849511286E-51.725584187750.324894454667-0.05676008990441.00333550986-0.03988580195730.982826915035-148.87088603433.050745437218.1261823392
380.03053001734650.1553421137050.183171646020.592357535628-0.1761563389890.8822136957760.1288558219780.432778012464-0.2229178863460.34426982997-0.106545476680.220433657194-0.6262178553610.136851605534-9.50829815099E-51.258977415020.0735369186696-0.1337902142011.10863785540.03130472076621.20543317457-120.68832042612.281732244217.6595943893
391.409872191090.6978323942690.543136736449-0.03782104263380.524742287565-0.01665522188210.06914303659490.302796427843-0.09946285092880.424043363756-0.0221314501328-0.4108011510390.191526157989-0.259225062962.94090903588E-51.196849508150.069334988838-0.09027877491671.029647067970.0319729078941.17140199337-120.9798233936.3369501012117.2093385888
402.462075768830.336118877477-0.2393968149781.47786874480.6745950490261.78425091760.0806418431055-0.08708641041460.1271333631860.2674766556090.0901456950113-0.239913550816-0.389755380288-0.446821679960.0001092054150531.264097131350.05217453168810.05580774574160.8319309025380.04526868969650.959128458174-137.747921052-1.16879648018.93102459809
410.7552577098670.8275581033180.6721835681182.744524032520.2711379781522.45888074912-0.0455433406442-0.2123842541150.0219587405419-0.0587077220416-0.0741672944130.147926788259-0.160899361335-0.1315602014791.53083206679E-50.9463852496440.008087025874810.05314205660180.8510158708760.02731706734240.997460028852-150.255694358-5.169415414688.19020226906
420.5647264148750.222720878163-0.1825647941780.0310381136932-0.3180945836730.178675647401-0.4633940627870.3278597517510.560017041413-0.2872597698020.0217861983256-0.143985241253-0.1293937971190.0504165938039-0.0003290118220791.188774907290.047871800936-0.1123031033471.1017076618-0.03870609531751.24784322125-98.5749497974-7.8248135879821.6892926597
430.0744717368039-0.03111828600730.07909137506780.4047116843990.2161775299180.224784563309-0.304299714193-0.765214691662-2.36429951255-0.194402204416-0.0531321732884-0.02846727824110.196604285140.423714402975-0.0006528501545571.602355131630.187638338912-0.03272653167590.9444159871240.0905248824151.06663526149-106.23268621-14.258636944736.22930758
441.63301344169-0.3652267099731.563792167050.8039190524570.01871611243792.236611682-0.0600328943013-0.3742562466150.2850827210410.237532092546-0.3553564830980.4723963538780.00858655695992-0.01579686978415.09574018172E-51.284915268680.04712941257550.09207521877761.01491596758-0.1025723774880.837372091802-113.292448653-5.3060936434234.8633333535
450.75550338384-0.482489617780.1416070695080.7890521275840.4126958230060.0525074137759-0.1731996089450.007724042467250.184794696204-0.3351425070360.05119592000110.6101599564460.237941520637-0.26568632713-4.85556665306E-61.25465363546-0.06569645165590.06479498216450.8092077345750.008372607441540.906019804253-112.941993911-24.996464857320.7775444248
460.216368460044-0.08193972168830.1728523280750.1055331051990.173915193910.4151708586070.2344002888740.000307018847142-0.3486960278370.113418288033-0.3331039693550.0902591559795-0.3349196268980.4824481996450.0001900834063361.581251161590.04664865152740.1670797284061.02273798958-0.06642364915941.19587521629-110.112993062-34.92512278139.98977048362
470.0754666224931-0.184092687190.0552630111307-0.0119512374018-0.001794696005990.0365857987274-0.306737093867-1.37248194715-0.1549512172780.631905851183-1.30801837624-2.281712125361.262958618421.48686521077-0.03733371383331.523490735030.2068758950050.02846793200141.286653389320.1066790281341.06165174393-100.908127501-29.010207240426.8012542469
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 1 through 307 )DA1 - 3071 - 307
22chain 'D' and (resid 308 through 716 )DA308 - 716308 - 402
33chain 'D' and (resid 717 through 819 )DA717 - 819403 - 505
44chain 'D' and (resid 820 through 1140 )DA820 - 1140506 - 826
55chain 'E' and (resid 715 through 794 )EB715 - 7941 - 80
66chain 'E' and (resid 795 through 890 )EB795 - 89081 - 176
77chain 'E' and (resid 891 through 1040 )EB891 - 1040177 - 326
88chain 'F' and (resid 20 through 42 )FD20 - 421 - 23
99chain 'F' and (resid 43 through 63 )FD43 - 6324 - 44
1010chain 'F' and (resid 64 through 150 )FD64 - 15045 - 131
1111chain 'F' and (resid 151 through 218 )FD151 - 218132 - 199
1212chain 'F' and (resid 219 through 243 )FD219 - 243200 - 224
1313chain 'F' and (resid 244 through 267 )FD244 - 267225 - 248
1414chain 'A' and (resid 1 through 358 )AE1 - 3581 - 358
1515chain 'A' and (resid 359 through 761 )AE359 - 761359 - 448
1616chain 'A' and (resid 762 through 856 )AE762 - 856449 - 543
1717chain 'A' and (resid 857 through 1140 )AE857 - 1140544 - 827
1818chain 'B' and (resid 715 through 768 )BF715 - 7681 - 54
1919chain 'B' and (resid 769 through 788 )BF769 - 78855 - 74
2020chain 'B' and (resid 789 through 814 )BF789 - 81475 - 100
2121chain 'B' and (resid 815 through 880 )BF815 - 880101 - 166
2222chain 'B' and (resid 881 through 901 )BF881 - 901167 - 187
2323chain 'B' and (resid 902 through 931 )BF902 - 931188 - 217
2424chain 'B' and (resid 932 through 980 )BF932 - 980218 - 266
2525chain 'B' and (resid 981 through 1026 )BF981 - 1026267 - 312
2626chain 'B' and (resid 1027 through 1044 )BF1027 - 1044313 - 330
2727chain 'C' and (resid 20 through 42 )CH20 - 421 - 23
2828chain 'C' and (resid 43 through 106 )CH43 - 10624 - 87
2929chain 'C' and (resid 107 through 150 )CH107 - 15088 - 131
3030chain 'C' and (resid 151 through 218 )CH151 - 218132 - 199
3131chain 'C' and (resid 219 through 243 )CH219 - 243200 - 224
3232chain 'C' and (resid 244 through 267 )CH244 - 267225 - 248
3333chain 'G' and (resid 1 through 294 )GI1 - 2941 - 294
3434chain 'G' and (resid 295 through 743 )GI295 - 743295 - 429
3535chain 'G' and (resid 744 through 795 )GI744 - 795430 - 481
3636chain 'G' and (resid 796 through 856 )GI796 - 856482 - 542
3737chain 'G' and (resid 857 through 1140 )GI857 - 1140543 - 826
3838chain 'H' and (resid 715 through 768 )HJ715 - 7681 - 54
3939chain 'H' and (resid 769 through 819 )HJ769 - 81955 - 105
4040chain 'H' and (resid 820 through 901 )HJ820 - 901106 - 187
4141chain 'H' and (resid 902 through 1039 )HJ902 - 1039188 - 325
4242chain 'I' and (resid 20 through 42 )IL20 - 421 - 23
4343chain 'I' and (resid 43 through 63 )IL43 - 6324 - 44
4444chain 'I' and (resid 64 through 150 )IL64 - 15045 - 131
4545chain 'I' and (resid 151 through 217 )IL151 - 217132 - 198
4646chain 'I' and (resid 218 through 243 )IL218 - 243199 - 224
4747chain '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