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- PDB-8bu7: Structure of DDB1 bound to 21195-engaged CDK12-cyclin K -

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Basic information

Entry
Database: PDB / ID: 8bu7
TitleStructure of DDB1 bound to 21195-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 / negative regulation of reproductive process / negative regulation of developmental process / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / 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 / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / proteasomal protein catabolic process / RNA splicing / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / TP53 Regulates Transcription of DNA Repair Genes / 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 / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein autophosphorylation / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / protein kinase activity / nuclear speck / cell cycle / cell division / protein serine kinase activity / DNA repair / 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-RS5 / 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: 3.245 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

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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: 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)501,14246
Polymers496,5589
Non-polymers4,58437
Water0
1
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,01515
Polymers165,5193
Non-polymers1,49612
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)167,07716
Polymers165,5193
Non-polymers1,55813
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)167,04915
Polymers165,5193
Non-polymers1,53012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.683, 248.683, 218.597
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_2chain "H"
d_1ens_3chain "C"
d_2ens_3(chain "F" and resid 20 through 267)
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_2THRTHRASPASPBB715 - 10327 - 324
d_12ens_2RS5RS5RS5RS5AK1202
d_21ens_2THRTHRASPASPEE715 - 10327 - 324
d_22ens_2RS5RS5RS5RS5ECA1101
d_31ens_2THRTHRASPASPHH715 - 10327 - 324
d_32ens_2RS5RS5RS5RS5GIA1201
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(0.267273639913, -0.931298782347, 0.24748207896), (0.080912126482, -0.23422889165, -0.968808574541), (0.960217698856, 0.278961295371, 0.0127501564258)122.745579701, 105.608065673, -72.1957577571
2given(0.21811663799, 0.130298225252, 0.967185351796), (-0.923164514743, -0.293890225474, 0.247781787245), (0.316531848242, -0.946916526346, 0.0561843499685)29.3695227717, 159.700433868, 68.1763140001
3given(0.242862149177, -0.926640640033, 0.286975784233), (0.0864536756823, -0.273980044499, -0.957841686907), (0.96620067194, 0.257433602033, 0.0135721069287)121.933066225, 106.819423417, -71.3915877761
4given(0.218209951837, 0.118893859366, 0.968632369439), (-0.926544837689, -0.286417416046, 0.243884660315), (0.306429568858, -0.950699381503, 0.0476613610677)29.8585026443, 159.834561721, 68.7845201961
5given(0.222391306328, -0.923481370577, 0.312608805165), (0.0715449123743, -0.304315908961, -0.949880599374), (0.972328870487, 0.233610756923, -0.00160681879291)122.442124159, 108.428463498, -70.5565371852
6given(0.22836482635, 0.102912861702, 0.968121092107), (-0.934371471432, -0.256176619731, 0.247635806938), (0.273494898419, -0.961136037405, 0.0376571127382)29.9380851768, 159.437934511, 71.144691485

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Components

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Protein , 3 types, 9 molecules ADGBEHCFI

#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

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Non-polymers , 3 types, 37 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-RS5 / 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one


Mass: 473.352 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H22Cl2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7

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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: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.245→215.366 Å / Num. obs: 110959 / % possible obs: 96.1 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 3.245→3.396 Å / Num. unique obs: 5549 / CC1/2: 0.385

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Cootmodel building
STARANISOdata scaling
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.245→72.87 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2189 5472 4.93 %
Rwork0.1921 105452 -
obs0.1934 110924 90.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 138.44 Å2
Refinement stepCycle: LAST / Resolution: 3.245→72.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33718 0 263 0 33981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004634664
X-RAY DIFFRACTIONf_angle_d0.814746888
X-RAY DIFFRACTIONf_chiral_restr0.04845169
X-RAY DIFFRACTIONf_plane_restr0.0055985
X-RAY DIFFRACTIONf_dihedral_angle_d11.70812902
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.02293541228
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.08633588597
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.799615103807
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.782313462046
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.695308683764
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.583571558795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.245-3.280.3461130.4073272X-RAY DIFFRACTION6.99
3.28-3.320.3382380.3789939X-RAY DIFFRACTION24.17
3.32-3.360.3923910.35491901X-RAY DIFFRACTION48.99
3.36-3.40.37281360.33222655X-RAY DIFFRACTION68.42
3.4-3.450.32261680.32073054X-RAY DIFFRACTION79.03
3.45-3.50.31491350.29423327X-RAY DIFFRACTION85.95
3.5-3.550.28871930.29713545X-RAY DIFFRACTION91.66
3.55-3.60.30642050.28843741X-RAY DIFFRACTION96.31
3.6-3.650.31861910.29943888X-RAY DIFFRACTION99.85
3.65-3.710.33882020.30913855X-RAY DIFFRACTION100
3.71-3.780.32252020.29053891X-RAY DIFFRACTION100
3.78-3.850.30662230.27423835X-RAY DIFFRACTION100
3.85-3.920.28011890.25053859X-RAY DIFFRACTION100
3.92-40.22642200.2283881X-RAY DIFFRACTION100
4-4.090.21421910.21573925X-RAY DIFFRACTION100
4.09-4.180.22982180.19873849X-RAY DIFFRACTION100
4.18-4.290.20381750.19553919X-RAY DIFFRACTION100
4.29-4.40.20871910.20273865X-RAY DIFFRACTION100
4.4-4.530.22522250.2083917X-RAY DIFFRACTION100
4.53-4.680.22881900.19753877X-RAY DIFFRACTION100
4.68-4.850.20932200.17173889X-RAY DIFFRACTION100
4.85-5.040.21062230.1673878X-RAY DIFFRACTION100
5.04-5.270.19781790.18043937X-RAY DIFFRACTION100
5.27-5.550.22881750.19053932X-RAY DIFFRACTION100
5.55-5.890.22212010.19653940X-RAY DIFFRACTION100
5.9-6.350.23052300.19513893X-RAY DIFFRACTION100
6.35-6.990.22361990.18623953X-RAY DIFFRACTION100
6.99-80.21442250.1753935X-RAY DIFFRACTION100
8-10.070.16342260.1293975X-RAY DIFFRACTION100
10.07-72.870.16381980.14034125X-RAY DIFFRACTION99.49
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)
10.64181660476-0.380140191948-0.1524776170492.85716877040.1031636354191.475228079970.0812561338659-0.396284844209-0.09181808322180.302957552545-0.1178037788830.3305576757560.138867033554-0.380450611671-0.0168386893181.10119214052-0.08619279887570.1236067620751.530134036410.2301026499131.3258925237422.019508662353.185099056564.2372937273
22.08001254622-1.17821187879-0.1341916407331.17457412627-0.100951830640.7409651169090.120374903924-0.507581559351-0.06872600160590.5180841530180.01180847641110.03467451212680.15261309647-0.132262186803-0.001573552591451.40691037512-0.0375939820273-0.006364782349691.537728616020.1476878983761.1003883528445.407634465158.021670127975.8943721686
32.96188683567-0.32366674628-0.9571504273071.97521987250.6006416602520.7300270098170.13957909531-0.07026757921360.0954648576501-0.03077574923840.000709214818326-0.151884216408-0.06601314666780.2162518239060.002256693774631.094472372920.0490383646562-0.08666451653391.162688879850.08331282445670.97683214414160.755942293267.158504543858.8290733874
40.88626581920.5772169353290.06961216574471.592770950980.05587602763381.374427905230.10724873366-0.0654436794635-0.5358191729870.1186867482130.0670201364296-0.1718046544020.4411199913360.02909282005170.05643083371391.313556312070.118637279884-0.2001025435711.238868342150.229630156861.3054220822955.81395256136.867072777158.0288382684
51.42603197232-1.00766714602-0.4018457329121.611460384250.6215898821462.11030763450.15316937014-0.303783202877-0.0978214257865-0.2242712306130.0911146146583-0.2692177358430.1097037520340.235169363374-0.02558605002521.299509012750.0670487520917-0.07550457050141.219634824760.08212744004321.2455037465657.601686597238.094761970223.7053970723
62.97854430162-1.07102147327-1.699548290051.65414948-0.8261148377782.453444830130.06453058442860.6608837760510.0654409660758-0.200665885262-0.1015512284320.2487675555480.22748534856-0.0963428484959-0.01006925599661.220288738920.0999494755041-0.2805781358031.228960534560.1161583850341.2045537145738.43267645939.171803031121.8698411782
73.337433361870.3339768463160.2867480958561.69988553877-0.3649461746772.468212451470.0674095920543-0.206107860234-0.343185606146-0.21540009754-0.01304184002490.2751185832830.404833155566-0.46334975113-0.108345864231.394924068140.0120667701214-0.23048229171.265820396330.19413434051.4586617939528.299623936636.085208750732.1650353242
84.77175232067-1.28463824089-0.3370929065482.23223864287-0.8332699656581.77089068293-0.4493954423930.2555915747420.182222254043-0.1104173595760.556681112601-0.02927752139550.03724585113230.164828554835-0.1057829579961.262256607720.080360869767-0.1184461207261.2908929757-0.04844691738511.1488138647365.317823763132.3329878492-5.98559841512
91.29148285695-0.326678964681-0.453629310431.057443091870.07636495317252.231102642830.1564618587020.442780850148-0.535930124307-0.604990329701-0.144265855891-0.04510205011520.381929483612-0.1220004075250.002228287259961.344822547720.114468317622-0.2378175588251.03886074738-0.009776233156011.4046412648459.055339121419.91166565051.03340707695
100.6175268992-0.08235053695430.02129063162531.40430259285-0.2144592806171.03631529665-0.117761070957-0.412848498078-0.6734406643350.7385075610310.26815077264-0.2394217141620.675049538414-0.0324934074268-0.02111161142351.485979388310.244927449412-0.1386232047331.272515297420.1430467580691.4628582359561.426206827514.204343755610.1742484896
112.14161552893-0.3376950202810.4011403598320.115447762402-0.2329123427651.475144428610.134877300759-0.096560026965-0.363986161581-0.1470487195780.03353884720420.389556330330.277080574927-0.157961410735-0.01609422592721.229586442090.0678257897283-0.2480968088941.217155758680.001355322336841.386933716443.493298538327.3123868761-8.09123724153
123.94724239626-0.5236756064650.2086936686861.0549277181-1.219153024981.286349848250.5375718961330.7594893653130.226867972502-0.733168496975-0.5927586090860.1819474837840.002637702989260.3334071107450.02478899116471.24565416181-0.0149604624459-0.2042468318791.358077888110.1305384511781.5209438794736.056597816835.9796260885-17.7399888678
131.98528709418-0.53278813843-0.01882756621341.854786147571.234427906751.41888354985-0.376050121380.606201362374-1.55864709921-0.5941294746920.0576412834761-0.7796096453010.1449970849740.667000772027-0.04378324973361.407105272720.348449263181-0.1433123244711.42243521733-0.002236041091521.61309381950.962798522422.4369947018-18.5683443513
142.361680121940.9334661981540.2030916438921.14986360198-0.2704931778851.35352590664-0.002731091754580.466839329241-0.207602704329-0.606249313672-0.0334810821090.03679298971580.387331064782-0.00754052200464-0.03107759374861.572701510540.292176481728-0.04675360436951.23385996292-0.1271864335611.0882638187495.006853629232.7162183-35.4046632358
151.308455224210.678145940269-0.1462661617681.468809179480.3730797422452.125243113940.1964988873050.00832699332511-0.211872845568-0.00336546373283-0.200563841919-0.04860813990140.359087762157-0.0416912266462-0.06447738905271.222082391560.164620466872-0.1176890676720.9448811739930.1237893758331.1688185965994.558240282828.7790390165-3.74293064852
161.111783043850.360519666416-0.772587221840.7451144059950.02595823574632.17083554781-0.006616357191210.0263209185096-0.08068716741730.0702174201959-0.126798652889-0.354781085819-0.09714012852150.645721336584-0.07108047456151.123135554260.147945389684-0.06575278847421.172635664020.1849718579851.23743777717115.1436659145.1107044129-5.51814591488
170.6625527096251.35572582482-0.253856820634.04195364247-1.066146577332.116298281180.366458151408-0.4540445725650.3158896677980.105231589763-0.3508042768250.287277323325-0.0969681319377-0.00234857573488-0.01229396597811.27590390439-0.004505301845460.05074715161261.17532325040.1016617575871.36436856521108.96880692178.9603588334-1.82646100104
181.10573985460.2300486715680.8411045219061.053761850490.4709395726732.59577605984-0.0740779031853-0.0427289768118-0.6397290084350.121345695632-0.1203913723610.2797826198780.3924984843220.287000870788-0.01409114145731.13653908710.08893045659290.06715973010181.125587911810.06076650069751.11090640051103.84065633284.2775766015-12.1214344811
192.813203496120.5968039185520.4767870826892.40356732464-0.6385383040011.85300476790.175635660129-0.2315187783370.8028795283930.538851465717-0.5860541870211.010169344230.547772274178-0.0001850816917-0.1115305022551.249012846080.03005509900330.06409837486061.000009391640.1707473090311.12708163503107.85170243574.2965209949-6.21861295732
202.62669914033-0.9694282158751.138825412212.857744918771.016884349072.554428059130.01731773304610.03110264039460.586420034581-0.5843913538280.099654130584-0.0349774685401-0.2797739743250.0982628451284-0.02066844106431.060505624210.09899903184870.05871549579191.232694530480.2399072558011.15330824941101.37097889278.5532796009-23.9300579924
210.7608924795150.236994521535-0.6165442664190.792392146284-0.4852436563680.5891167868670.5256410056831.065286157240.139062005061.08742446904-0.253827499872-1.10507974831-1.240464655651.365459225990.04714406778781.324859486320.07302253742630.1317595310071.989071467080.2709423113621.78309663905114.16898887276.1751468305-32.4055567981
222.216339973091.507898611690.3005589917532.491847454050.9747389844992.489144785630.2728826995710.8125851432640.0180569180219-0.4438328575540.0544471779717-0.1951281383130.1244308397130.622170602596-0.01534961501131.329238451770.2616494393560.08628922305841.530644032450.1970788945091.11021714096105.80904962569.4225055279-38.8442533974
230.1365679900660.168460819812-0.3960224191260.378818149378-0.01694435459930.665087204643-0.0812633223221-0.114398734261-0.559651242188-0.4161079760140.690922674601-0.2162780226190.449554435925-0.2300314908190.06055889529521.627381295180.0237391745661-0.0501160107681.725765917140.0906178120631.9281204593189.987716579857.7294824253-16.3371254731
243.103631057730.4461197179581.718449304812.304081334871.403991555214.65242869483-0.356574116065-0.4550111583130.6955726096360.0129251580729-0.2853367194021.03838127419-0.636272527509-0.3337832052110.0704308581321.31373768280.008800898494540.01024521997261.09847204747-0.0446561197131.29903061834105.259395897108.9326672930.5526552845
251.05442792372-0.353265153535-0.03370266980441.537290606770.4947040850221.44353774802-0.1329760174740.1466824464890.197213013501-0.450339223663-0.109109376451-0.272818542922-0.4977961620780.453860005895-0.05670309211460.937040271686-0.03551698919260.08094192901141.124914646780.1626765080741.24680647349116.838938484107.558727145-10.789043499
262.510461164790.7219285857640.2593439465722.54145794417-0.1789540943822.735048113030.027693853954-0.0969556121195-0.4662366935550.07389408856-0.186261476257-0.6500385887980.05361874389130.935927707455-0.04476535103760.9381095595180.03064942572230.05070745892771.174606021140.155855611791.13645956985123.64378231499.9412695623-6.37707091817
271.06626477943-1.314843469310.9849318549371.42633241329-1.594922733182.72555358433-0.1589203929670.514725502831-0.0510292471295-0.305474840614-0.017921141568-0.229317672981-0.0259139189388-0.103655634383-0.06437065329131.094714573260.03997148724640.0406562218151.083225980610.08226926806171.16881679821105.568142781109.132387629-24.2393151591
281.60555642330.02832253093240.9240216611760.6906007488470.3314484943772.42695863362-0.262014817474-0.03721133768930.335290559247-0.0865157715123-0.05419941865820.189964459637-0.360960473765-0.62010156255-0.04216184493651.014170002730.0352468178825-0.001113298723941.168158850310.08640493781741.0439569547197.393333372116.808282473-23.1276787397
291.67489415825-1.401077915080.6796899587073.479582850522.545306600784.406070487490.3408132045640.427667445012-0.4383191701170.2617507542660.5013911477210.6907554564720.109352592722-1.827949583410.006849893468591.11889951630.01057897255850.09034643954431.40901387020.07098477769931.3351972518391.0758960242112.661755319-21.6494624891
302.445332634420.409630036162.305751132892.916950066080.3685186941063.934954907750.08910260793470.2041091835161.095772462970.617164613188-0.321325098946-0.387409782109-2.049189063961.03627797311-0.06753032237641.2226171782-0.254153516885-0.08731247506411.337890244790.1516159568191.24674473969107.339695793122.778214331-15.7123385091
311.34520252617-0.00266453975131-0.1605016937260.989658654421-0.09244049785233.158469568530.167624039875-0.1312576408190.525239482054-0.0389398980437-0.0310292035588-0.239528496965-0.3814199955760.308446982003-0.02139328014961.09876451558-0.05298626352990.03963669732531.18894939881-0.0981428805441.3602548768102.817302636139.90436712329.2196988114
320.468864105515-0.254919447727-0.3005756429831.98675389775-0.304807055691.75659997235-0.197291186701-0.200637916449-0.0304369323508-0.1645431861080.154381711257-0.4711426846710.07744793640010.4914381152980.003336499180460.9180500883730.1608893514490.03157793271151.43370260846-0.01610227628131.29766006278114.763844582111.48663596127.1192261516
330.7925127653670.0909074837379-0.3599664224742.105364063390.7809625291351.56267556289-0.107780235962-0.634307559191-0.1375111277460.4263517907410.0680095229947-0.1330413876270.1263284997370.389657542054-0.06743054687431.021714644790.224591386869-0.07377602556691.53753672510.03481525009511.08734485877102.728884604109.5327110851.7791323895
341.73751631592-0.199158373260.4100925652112.070267615440.0004418277058081.03509009806-0.0160740938338-0.184926253942-0.466756008273-0.156178341875-0.075789896387-0.009011993208430.179172191722-0.120220364881-0.02873902892781.205453161410.1059820803580.03175369613411.2298105405-0.05175737625111.2395764484567.954014154999.351287795252.6131806777
352.290759428380.474321540319-0.6736634249823.3667497016-1.946681273282.201732548080.0767245409073-0.0299264281808-0.111739603855-0.169846025002-0.1668979548350.04395843831140.00871301003687-0.02730031378290.006243253033580.9664340817280.126093387509-0.0446673088761.06048397564-0.1172154442181.0291267349567.9105023731114.40526760745.5571041652
362.22482763351-0.744584987949-1.083948316812.434725819820.9316519261522.1249623533-0.0721598611224-0.191732299620.6536393873130.2042686118190.0129496293572-0.0726779107732-0.3604083268550.155714595688-0.03179124078881.027976066990.105263835368-0.0514524705811.07008720403-0.1439226251751.1457667659469.9261106063134.80297757548.864464252
371.78166086648-0.190615922603-0.5457742749381.50409640057-0.4427203565090.5379970618160.4464648484210.5802179963220.15579159285-0.336350805538-0.814204095881-0.4803411273650.2651643578990.306048834163-0.08128460155871.167168633840.244071350799-0.01092912340571.348800148360.1432224069271.269739110176.8228163319118.31357954330.2294615344
382.001196778930.4850186229080.2021128319764.46213796814-1.901462579283.240804028410.1371565909270.323450518705-0.13371109846-0.504054822960.1779271446440.8239238561780.240299460934-0.5622120271030.009387974471251.135524101030.08848776607540.01109220699751.306183101620.05166763720651.2356809943742.432951445388.696186368757.6496885047
391.667793819251.00652534990.07701640025412.85810805832-0.6389374473360.2917078221050.272862183011-0.8508354053440.7774643473721.04781101493-0.4782057351551.553431629650.220348631701-0.942245901110.05366803678191.207469199860.1655493916390.04001119979311.6353538175-0.02828144119741.2704564703140.941337873398.805490080871.8953621736
402.401249674640.502940021261-0.6215028818612.127526462930.0006154563876792.14195196064-0.082935376228-0.4228708498990.0009945828342680.698314528751-0.123732346626-0.06746326564220.01177479761840.17833818942-0.02181813360151.184199257260.109328318541-0.04580138887571.26446715333-0.01439391127140.93048526238352.2038351844100.33687080170.5218364344
412.7328969858-1.243130721890.6857037184351.93295339771-1.291353488751.229487567910.0247811993052-0.2612550864580.644338061799-0.123009479611-0.212543700781-0.315223304867-0.614657712026-0.311928108479-0.02038974435611.133031477750.17421083122-0.09664322010571.25617177003-0.131017964621.1590982043136.2549110595112.55332661857.1201419471
421.21780744448-0.4857235330570.6191324850942.58539245084-0.9200595228531.50314378343-0.1855595088740.1943594210240.106419056325-0.0319764726646-0.003564921075230.557908685090.188928623765-0.3225210134660.012765740031.065739746290.2196010812340.03662442915331.20047694476-0.1272472513321.1177204572431.5887072957104.43767797155.3736955126
431.20584372717-0.8683668771330.6204920251392.058978593640.7048672448763.44934210813-0.157675564487-0.7445359041410.3021134904790.252539139774-0.02330389582980.5378655687030.417251781415-1.603285858210.05723922542011.345253313930.132657459045-0.06313356099641.49176141444-0.1282541682951.4122718424521.4687242871115.03803540746.1210080888
443.726202131333.069125864780.361033261974.46391233469-1.603645059382.263892767910.4866606265420.420366555755-0.247383397883-1.426942969660.0836445675874-0.359968434216-0.4973872838020.126858839803-0.01563779376731.372868407610.102712574214-0.2131490563221.43418932439-0.2279645238411.1496862556530.0371407802107.72264806844.1546722297
452.876141659-0.354939289761-0.21195511343.35162938248-0.7665058565065.06886381611-0.280528181296-0.0974220524121-1.276684797981.191658892220.3512648272241.124888218090.867390041885-1.187331259030.0512909048391.321814222680.1036344981360.01058302522631.572876828230.03129749575831.2857460778425.8267832896101.41433359762.8713257688
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 719 )AA308 - 719308 - 405
33chain 'A' and (resid 720 through 856 )AA720 - 856406 - 542
44chain 'A' and (resid 857 through 1140 )AA857 - 1140543 - 826
55chain 'B' and (resid 715 through 832 )BC715 - 8321 - 118
66chain 'B' and (resid 833 through 892 )BC833 - 892119 - 178
77chain 'B' and (resid 894 through 1043 )BC894 - 1043180 - 329
88chain 'C' and (resid 20 through 42 )CE20 - 421 - 23
99chain 'C' and (resid 43 through 106 )CE43 - 10624 - 87
1010chain 'C' and (resid 107 through 150 )CE107 - 15088 - 131
1111chain 'C' and (resid 151 through 217 )CE151 - 217132 - 198
1212chain 'C' and (resid 218 through 243 )CE218 - 243199 - 224
1313chain 'C' and (resid 244 through 267 )CE244 - 267225 - 248
1414chain 'D' and (resid 1 through 307 )DF1 - 3071 - 307
1515chain 'D' and (resid 308 through 819 )DF308 - 819308 - 506
1616chain 'D' and (resid 820 through 1140 )DF820 - 1140507 - 827
1717chain 'E' and (resid 715 through 768 )EH715 - 7681 - 54
1818chain 'E' and (resid 769 through 794 )EH769 - 79455 - 80
1919chain 'E' and (resid 795 through 832 )EH795 - 83281 - 118
2020chain 'E' and (resid 833 through 892 )EH833 - 892119 - 178
2121chain 'E' and (resid 894 through 914 )EH894 - 914180 - 200
2222chain 'E' and (resid 915 through 1020 )EH915 - 1020201 - 306
2323chain 'E' and (resid 1021 through 1043 )EH1021 - 1043307 - 329
2424chain 'F' and (resid 20 through 42 )FJ20 - 421 - 23
2525chain 'F' and (resid 43 through 83 )FJ43 - 8324 - 64
2626chain 'F' and (resid 84 through 150 )FJ84 - 15065 - 131
2727chain 'F' and (resid 151 through 194 )FJ151 - 194132 - 175
2828chain 'F' and (resid 195 through 233 )FJ195 - 233176 - 214
2929chain 'F' and (resid 234 through 243 )FJ234 - 243215 - 224
3030chain 'F' and (resid 244 through 267 )FJ244 - 267225 - 248
3131chain 'G' and (resid 1 through 294 )GL1 - 2941 - 294
3232chain 'G' and (resid 295 through 819 )GL295 - 819295 - 505
3333chain 'G' and (resid 820 through 1140 )GL820 - 1140506 - 826
3434chain 'H' and (resid 715 through 801 )HM715 - 8011 - 87
3535chain 'H' and (resid 802 through 892 )HM802 - 89288 - 178
3636chain 'H' and (resid 894 through 1010 )HM894 - 1010180 - 296
3737chain 'H' and (resid 1011 through 1043 )HM1011 - 1043297 - 329
3838chain 'I' and (resid 20 through 42 )IO20 - 421 - 23
3939chain 'I' and (resid 43 through 63 )IO43 - 6324 - 44
4040chain 'I' and (resid 64 through 150 )IO64 - 15045 - 131
4141chain 'I' and (resid 151 through 194 )IO151 - 194132 - 175
4242chain 'I' and (resid 195 through 218 )IO195 - 218176 - 199
4343chain 'I' and (resid 219 through 233 )IO219 - 233200 - 214
4444chain 'I' and (resid 234 through 243 )IO234 - 243215 - 224
4545chain 'I' and (resid 244 through 267 )IO244 - 267225 - 248

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
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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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