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- PDB-8bub: Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K -

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Basic information

Entry
Database: PDB / ID: 8bub
TitleStructure of DDB1 bound to dCeMM4-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 / biological process involved in interaction with symbiont / [RNA-polymerase]-subunit kinase / 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 / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / viral release from host cell / regulation of signal transduction / ectopic germ cell programmed cell death / positive regulation of viral genome replication / cyclin-dependent kinase / 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 / RNA splicing / proteasomal protein catabolic process / 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 / rhythmic process / cellular response to UV / 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 / chromosome, telomeric region / damaged DNA binding / 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
CITRIC ACID / Chem-RNU / 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: 3.42 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
F: Cyclin-K
G: DNA damage-binding protein 1
I: Cyclin-K
E: Cyclin-dependent kinase 12
H: Cyclin-dependent kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,92119
Polymers496,5589
Non-polymers2,36310
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)166,2436
Polymers165,5193
Non-polymers7243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
F: Cyclin-K
E: Cyclin-dependent kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,4357
Polymers165,5193
Non-polymers9164
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA damage-binding protein 1
I: Cyclin-K
H: Cyclin-dependent kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,2436
Polymers165,5193
Non-polymers7243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.861, 247.861, 220.715
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

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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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-RNU / ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide


Mass: 339.433 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H17N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
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: 0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive

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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: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.417→214.654 Å / Num. obs: 89624 / % possible obs: 96.2 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 3.417→3.611 Å / Num. unique obs: 4481 / CC1/2: 0.39

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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: 3.42→60.04 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 4460 4.98 %
Rwork0.2118 85099 -
obs0.2131 89559 84.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 157.55 Å2
Refinement stepCycle: LAST / Resolution: 3.42→60.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33702 0 157 0 33859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003534564
X-RAY DIFFRACTIONf_angle_d0.581446741
X-RAY DIFFRACTIONf_chiral_restr0.04335170
X-RAY DIFFRACTIONf_plane_restr0.0046013
X-RAY DIFFRACTIONf_dihedral_angle_d12.820712966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.460.552170.579980X-RAY DIFFRACTION2.49
3.46-3.50.5284170.5016495X-RAY DIFFRACTION14.55
3.5-3.540.4727690.4551090X-RAY DIFFRACTION33.44
3.54-3.580.4371840.41031577X-RAY DIFFRACTION47.51
3.58-3.630.4164690.3791890X-RAY DIFFRACTION56.67
3.63-3.680.33911220.34842183X-RAY DIFFRACTION65.3
3.68-3.730.37371370.32282375X-RAY DIFFRACTION72.37
3.73-3.790.2861400.29662632X-RAY DIFFRACTION79.11
3.79-3.850.32671790.29252806X-RAY DIFFRACTION85.29
3.85-3.910.2971440.28223019X-RAY DIFFRACTION90.45
3.91-3.980.29321610.27163096X-RAY DIFFRACTION93.38
3.98-4.050.29181720.26783277X-RAY DIFFRACTION96.75
4.05-4.130.26491720.26073247X-RAY DIFFRACTION98.28
4.13-4.210.28151760.25993331X-RAY DIFFRACTION100
4.21-4.310.29071550.26463367X-RAY DIFFRACTION100
4.31-4.410.21551600.24123348X-RAY DIFFRACTION100
4.41-4.520.24042160.21593298X-RAY DIFFRACTION100
4.52-4.640.21651520.20263356X-RAY DIFFRACTION100
4.64-4.770.22871980.19823339X-RAY DIFFRACTION100
4.77-4.930.22231570.19613367X-RAY DIFFRACTION99.97
4.93-5.10.23042090.20323301X-RAY DIFFRACTION100
5.1-5.310.23791270.22133414X-RAY DIFFRACTION100
5.31-5.550.23121560.22933367X-RAY DIFFRACTION100
5.55-5.840.22591690.22143367X-RAY DIFFRACTION100
5.84-6.210.26691890.22283364X-RAY DIFFRACTION100
6.21-6.690.29131710.21463397X-RAY DIFFRACTION100
6.69-7.360.27172090.22183352X-RAY DIFFRACTION100
7.36-8.420.19051820.17953395X-RAY DIFFRACTION100
8.42-10.60.16991970.14113419X-RAY DIFFRACTION99.86
10.6-60.040.20311640.1733550X-RAY DIFFRACTION99.12
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)
13.300909108550.9582570419120.1311594956371.29206038707-0.1026938698711.3919352343-0.186977618179-0.472090295343-0.5535813308820.5565526522110.124192911882-0.364048951870.3457233553960.27717468185-0.01055587485041.676475430220.323515910098-0.4348289116481.29303999239-0.1352719471771.56396076524-57.012347703-8.2131404917726.5291388949
21.372529347580.9281576991960.179894194472.18893326918-0.2643354492641.07013369425-0.145123546936-0.8025466220170.4860458088890.7563481772770.166678786132-0.210799756499-0.0005400356133920.391183132143-0.01927619874671.839746618870.16207908343-0.3268883876141.53783188248-0.2566295386821.31811172738-72.87657680419.0014840434438.997499592
32.61199447070.686402083089-1.063507065814.18453704897-1.294208464140.6355795561540.002890701553530.10900146140.08730891526140.1757358541420.01015192932710.2702820714230.0772458408686-0.17132601314-0.01795538825421.450341273590.00394124356771-0.1273643510461.01187542905-0.1232511956371.19069353118-88.733221827315.4652696124.072366926
41.89119916276-1.14443343555-2.236971574122.95629773253-0.1245921995533.881202779020.3531539316520.1297009622140.628416657583-0.112165723266-0.0357016369223-0.202869351705-0.272066459540.181803556083-0.0546808567871.419288569920.0471993669978-0.2557027079341.00667013076-0.231767408161.19563800354-78.639749856330.72832984613.1419374541
52.153721906720.2940076052190.4062128674512.179257374970.1824244993952.588246075030.1980490035480.002722242806450.3879405831180.6091008584080.144213268578-0.401069627419-0.1883877102530.580757490016-0.04466673228041.61441969151-0.0322810787389-0.3852262769331.37321651332-0.3627002356391.6756634328-55.531858468629.628556483824.3046555772
61.118625487740.0800473422617-1.943308488410.4538448576870.128639773752.63557078895-0.301828939265-0.5764907778650.4596614510670.360272757274-0.211519088511-0.476547071192-1.215675543720.247811243577-0.02433790207741.91084739728-0.0190955247602-0.6801026915391.79862439259-0.3930364509521.99670030826-43.645408318725.189143406932.6114509469
70.6903933209570.0308929583216-0.8355810666910.690838283317-0.09282527448081.344731903040.08834001661030.2092453369010.1074605997570.3229254434490.217090103797-0.0287001349761-0.464693743788-0.0402108711534-0.04521274690111.68381083896-0.209469430869-0.2389901527081.41714059061-0.1373755023911.50821597477-61.784100218231.4137117381-12.6224336259
82.44827895669-0.24524462558-0.250474516752.48906220025-0.8379164723041.94468246135-0.1523483806350.09690660693170.128685006904-0.660439884758-0.121453688576-0.58261698763-0.0886624292827-0.219389334057-0.04410966526861.601431239410.00237252913771-0.1888734248721.36467342237-0.4679809513921.67856294091-57.288608080813.3424630769-12.3753724752
90.2995701841690.5911553941280.07616776554981.007314193830.1341444411580.002236880356371.24924262096-1.035126756621.688391732920.634958248146-0.00342791487359-0.48500826819-0.7118392317670.9521264756580.6517724617691.6089445766-0.381177688260.1801946817271.71614356675-0.4971390700462.68587042726-43.539369428722.0225788424-3.51833011892
101.88290862648-0.440193754723-1.29940352452.47523902565-0.3702554576042.40031033284-0.2443576644250.610755865432-0.47701560545-0.05346155816410.205747479616-0.63126936934-0.1524524526680.629253403958-0.08165441327461.299734865340.0852403310001-0.1202310537341.41649383939-0.5387999728411.84182690332-42.73838067014.41286727925-6.24829642509
110.896704997289-0.3890845180150.2875626526180.147562745163-0.07601511295330.100397997628-1.46153852814-0.6292254969520.4868795103660.411131571680.5093218726640.8369312878250.06923225218560.320732376198-0.3479271753271.818077343630.248154342426-0.2820747409412.08532710691-0.2411869294232.13303570783-71.621984932410.16976010495.63849006866
121.36782354223-0.1947138357790.7821003239343.82208379376-0.4749804395731.130458503210.1793543650520.362819395679-0.080005808189-0.378830810955-0.3491414563990.9034195453970.5290685437770.657332379421-0.1354320455591.49942170305-0.0734440824740.02887199906011.29937200442-0.3111668451771.37896208491-60.800029821640.0351084473-42.4713379091
130.438184644795-0.6515830676780.5566998485621.85629044834-0.4649407143851.70241439226-0.03997457372910.64883158667-0.43478862613-1.396052558950.497766827424-1.312503379861.155904741380.8004297683780.05104809021851.34801334177-0.3086232682120.2413025613991.41049062224-0.4835979972951.79954953912-43.208036866742.6441294366-40.6493245085
141.395098264250.222617719948-0.4605823602161.6890194718-0.1756950558042.8423104374-0.217664519701-0.0716412453450.09056711322310.2343694091960.144264167983-0.831447891623-0.09801651214430.295541497955-0.002212001003111.18619750763-0.187308287977-0.1010917594371.21198683432-0.2671901336811.71161624647-45.523596724140.2288429003-31.0790038603
150.7146516249610.7933580336360.4277802494691.82099667617-0.4311891877221.01769625793-0.125822449164-0.174930108281-0.3088472090610.403070729309-0.120237767243-1.02609892638-0.6128107497060.223291292105-0.0540148094221.58171265562-0.1463049690660.006572552493441.17995085171-0.4248673172681.67502141552-46.265048213749.2000703872-27.2528790026
160.4911965806-1.22192603319-0.5466173162692.226263988591.29694562392.20496706360.362947746611-0.502739696730.1116203415980.5318130496680.15378906024-1.77494061146-0.256815217150.02452745522540.05727465345071.26665029629-0.1427319520620.2118905951421.32479890101-0.2963986710641.82698544535-47.888271016521.1103384524-37.9062853509
170.756052140244-0.4662341892160.3234891013982.106134938-0.240253367310.981948353003-0.2665033256950.588389517745-0.6438862753820.272642958196-0.0893550858299-0.457341948849-0.02209992132120.043082773727-0.01924019768051.499530416920.02317207143770.1587420060691.36183627634-0.3805472849591.84043164975-44.447743285924.6941862994-48.2000032147
180.902828388939-0.7437455642640.68856443923.01482075784-0.03432235896820.5297209900580.118814718890.52564420749-0.117537129852-1.13499228028-0.00156624720916-0.4121446354450.289101341154-0.1069991168270.02064089086441.46941744088-0.1090613153750.05795829580841.47543099099-0.4676927786711.86197008178-50.150614543512.1030889265-53.4147066653
190.425879577351-0.0263787571623-0.4970185104221.56203792968-0.6949212489130.951824748415-1.231506542840.3598424947711.14138491024-1.08492247790.19281712063-2.244769117-0.4110241628590.91931465894-0.02657491678011.893703454820.0354081015798-0.03321034547831.82419150358-0.1765337761782.12083811879-45.263531651731.8584721521-55.0691913195
202.47771916712-0.8694558042850.2295567629961.9734507231-0.2128642119481.12245419290.003541348093120.4574740045850.0613787507351-0.7636987200790.124209039516-0.492250211334-0.3195776298480.504751916546-0.06447820439211.88874057856-0.2582321751220.2453640945931.24022595481-0.06947275487851.17564262659-74.125125625566.3605752856-69.9930177316
213.32903648974-1.42220763313-0.01237407193041.4462811722-1.243948275922.47916914459-0.13107149142-0.5149974084810.212677890430.03489925613310.214508850027-0.763253168649-0.3446118452210.245928824953-0.05895152364421.28783053115-0.207572437369-0.08692361663251.24912236211-0.3128721282251.19289040778-75.188150740766.1574438995-35.1445756568
221.482413946420.05926164034780.1147799892271.7272377841-0.8824148328082.971435105470.0350234468901-0.1417679989440.395884936585-0.136974948920.03453788242960.322781777077-0.632069780821-0.341368999823-0.1335480904261.34879359071-0.0172520175168-0.1147673710130.989932781147-0.2232826065731.24425194775-96.259893996777.2395117496-41.5786269943
232.77532725784-0.404112629384-2.162327922312.520510936940.3759613284063.45757303804-0.9094196196520.379188023809-0.5416865482890.6769162196290.5940689301690.04650432195930.661577911269-0.318454299946-0.07818638072231.324694986320.0399310159788-0.02606755289151.165526507930.2461874101231.32760283772-146.43586994236.6722417435-36.041299424
240.8192559665111.13888156492-1.586681754032.61633152322-1.695124852052.72642077123-0.5638994516140.256749771278-0.0499059573254-0.5158792307240.198857014639-0.3073475682440.793831431555-0.602866470279-0.2239698974391.105917887630.221884572778-0.007893438694171.109304530690.05371997120791.45521847465-156.41738971147.4289691899-45.6504727396
252.062088275880.7907129594460.338874857143.42735141902-0.2824735662650.872688326859-0.5783086143780.104230490448-0.3960275785260.0463557239945-0.1200456076480.2032063052530.442772974657-0.533119222071-0.1294413109480.9670829094730.18024396318-0.08800928970670.8913555988490.1240547572071.0900742828-146.88637918149.6987718186-44.6111190841
262.45238558702-0.1288173662430.1442042811582.233210375370.4826876129372.18175902803-0.1339988834380.1825459954070.515537318430.0008243857499740.0557095558436-0.168574441667-0.971831639282-0.15316364158-0.2217239785431.320324051350.102998164972-0.04086403943981.193507236330.201576944631.0035780547-152.5216358660.9319994917-46.4789181696
272.86843839818-2.90235012951-0.6293916987035.93294445350.003471725314320.884813330836-0.137989051197-0.2737790188830.7475693254790.352549057427-0.952934201839-1.36347960106-2.199010682320.162898529577-0.08984312327291.308052461420.11517380796-0.2616543869770.945947942476-0.1833918016331.32315093216-141.91309437357.7072005476-38.9081529046
281.052299896460.7876352437580.4409341650892.095008032042.208882930942.839170959930.002540750191790.720211809962-0.0752392244071-1.19564066042-0.0132327179528-0.680423530714-0.7740111413750.17470571497-0.3384466378930.954319239740.0849745087822-0.1607148123521.057682347280.08641600400721.24582328658-141.15329033537.6468808151-58.8705094579
291.209995442620.1427640687180.2228945941072.582883516380.7931376623673.209374497390.1277917837310.2863738151760.03542382464950.2226302280240.09108489279360.5062064588420.328412824161-0.365112918878-0.1110511485131.13507100399-0.0878097643959-0.01144174346631.048843687680.09985439836861.15727772428-151.53031617433.4897292426-58.174665462
300.31543447217-0.7737449356760.1424695025061.71726727520.81037916171.76656693126-0.1950290335420.281972445944-0.7737721407780.281426514186-0.2678314801360.02293707410831.243498947980.123500109803-0.1738454545361.193016116240.1333951345610.02890114974360.870901866504-0.08040726231721.17202092419-146.3311804621.1464262966-63.8679555021
312.70312750869-0.32660979414-1.879084326432.212391233172.27023064953.371706622240.257373102728-0.999467757563-1.667774768651.812324771020.2855784518872.91466933934-0.838152952048-2.24730855871-0.1866613164951.33734719080.1856161579480.04165683946441.565549604130.09493432236661.53685457926-159.37273237131.2684430711-52.2304142305
320.2628635894950.592453286852-0.1840092180280.5796065149510.5497017868152.115051872220.0219682270855-0.08177952873980.3199753212910.3841994336530.08490877919671.10383677469-0.452076463349-0.587753022476-0.1307853799091.635506214340.333271872080.2794274993941.547049187070.2955047028492.18354857479-174.47535430524.70167351723.53669169746
331.905734046080.825519755637-0.01635591699921.368083009890.380425512464.001028859350.007600408763230.407522107332-0.599524315182-0.6747589076650.227778448351.100589486480.134226463833-0.904351160584-0.1785277953361.485918109340.161264246913-0.3196661206771.454518756410.2997663165832.07750988721-170.54078916515.3495152429-17.4695972278
342.221844911690.7586313100540.2201805319642.73899292663-0.9726466204091.47264785441-0.265904775842-0.1854008120350.8926055826480.6538740658070.2299665028621.2962424355-0.776679179869-0.428005136118-0.04607819214791.863442072760.3609013001040.1064228126941.090432501290.07569497800921.65547146774-159.47861634344.7099399654-5.01251504576
351.502196448022.308589715160.5473210957152.94075986723-0.1302325766853.624038672790.240624923741-0.02551586526580.08912756842670.211647692005-0.0932096758594-0.191502329378-0.7724420623130.248999627875-0.1517904360881.514599186120.0633331665452-0.07487625159551.159149827860.1244002471541.33293869867-140.19440566641.9685869345-17.699283243
361.582159824740.233617181434-0.1303307011651.32287747698-0.3085394085471.35431611069-0.163407817716-0.7523184379090.2279844711510.9631426562380.16665662330.223888101158-0.3500623176230.0403519187509-0.1586916761212.106659248840.209836706620.1023910703581.170083840250.01979171680531.27530641811-146.04700462635.039428207613.6623155148
373.25345110270.3794597878510.9286993724141.845743709720.6294247985053.05079900580.1863826585630.150200198329-1.09891112922-0.4213210718730.385817885603-0.3489888851740.478439559420.174333328079-0.04845252872261.809087238610.11747817824-0.08320444018341.002894822320.03176049481581.17902707507-98.2249386938-8.1809700976720.4623827705
383.212547334030.5861659080190.4827509756222.885864379950.5411913969092.05535326968-0.361278914563-0.582494974642-0.5438714693730.8115044725060.0151365468516-0.04343289361040.423491951441-0.180494339257-0.06444874615571.932662861530.2007985619310.2049513181181.08574917660.04594020995470.857362912788-111.531647065-9.9611824211132.8458943773
391.79700952517-0.1389501335030.4813901337360.5338781133670.6103671661962.688973010970.254681764932-0.9287023620350.9389061944850.450195460506-0.381209122316-0.08479287940290.130384935390.744672779965-0.07477065024321.993579161720.105759088513-0.2435829690791.18185449761-0.2822342238490.922921679724-111.035959738-0.83862609493538.0873366523
401.006701404690.7371937110860.2517219061543.651117582091.333250657460.218609139202-0.4060841977040.344588152966-0.257516671477-0.754580963134-0.2985813601511.74003033747-0.0563863736555-1.012438641-0.04772585121451.80387826766-0.1431263602130.175260775051.05028055499-0.1588677120231.3241495043-117.505452744-20.63253074716.5430625811
411.705138281.0372052730.5301708421782.238908726750.5368085291111.81508401705-0.826163490075-0.113211379829-0.429883254259-0.706221101220.555056853854-0.3807187393560.587297419609-0.499244157935-0.04540377191471.88311586822-0.05346715522350.307190580920.825377529125-0.1058566639131.24020664181-110.048177187-28.034775932420.8845660232
421.29754196272-0.5470777203680.6272365614111.8670849468-0.09631852301193.207405341270.332285734012-0.172156697454-0.3233591820510.8143189718920.6326035031890.07539426750480.8930936918221.66498181065-0.01180365699262.14493602007-0.08124835084280.3400474374131.4933976701-0.2763328979161.58169374081-111.053815172-39.04148235548.38998048932
434.744632052340.919982172655-0.3607187155330.6322961232240.6223018106371.0437773424-0.4263119884830.501051817298-0.317079278999-1.297209896330.06990100712820.09374942929230.7043966667-0.730307081359-0.07568644228761.96861965053-0.1669596349640.3515057335061.24473325117-0.2002926870691.12339617629-109.057971315-27.896070426.70042221164
441.723429842440.4353096355391.785109172042.571200647950.7164779684422.60043660455-0.394143337007-1.35160857326-0.2902255622820.140934121608-0.863630312515-2.019166203230.5024593962051.638657892150.03641877920732.048500037940.1722491942880.1465637413931.313394023480.1555144879621.52250371659-100.865341433-29.033688010125.0826807492
454.215289894911.307873141391.944057230480.556085031085-0.2103083334912.60525630514-5.51142199914E-5-0.386786564318-0.4504298655820.4299097411890.4656538709350.1940380203980.1762692899070.263420406122-0.09443286693981.305984343340.0341122352489-0.09149617841691.28633912289-0.04787257069921.52755082435-122.93378806155.6297695409-37.6583563597
461.42866590714-0.615188038059-0.9848950535880.1795048618170.3109656723760.9783391650680.416461919818-0.245967064054-0.1343607826030.157774159255-0.203973030309-0.7807914177390.543456829267-0.089403699998-0.06546033500781.20475062192-0.0291023673752-0.1468906062770.985048831158-0.0915547543221.42510948201-124.72998532948.4537665898-48.1982271811
472.8508150849-1.70235432345-0.3974341333042.68434085471.07350316462.97098419405-0.05070253334140.0540681983059-0.438715357517-0.2529409394640.06524153772930.524861353436-0.1671401431240.252680817863-0.1025961452621.034471064220.0242001931113-0.2714364241190.995876587098-0.159265141791.23444580658-115.83968652251.9940437358-50.9819299728
480.0734951418432-0.336096331134-0.4874687891680.6006392229650.8764740285771.882790890680.828191642426-0.07916821057972.002621658120.04868053802241.122342894610.327905773596-1.064093123790.5023402638880.221527893081.913808468470.1908704776510.1886149563871.57475654108-0.01858868055282.53690658078-116.551378665.3769110626-55.2858818176
490.106549170116-0.228562554590.2890028834610.288240058562-0.273225845970.9914270011461.208916075740.4796262081380.0544842997019-0.248969734304-0.7109356226570.793608496457-0.773941490832-1.07695615481-0.1476927622531.922503307250.326626200127-0.4775537579981.28554272745-0.05439579948391.62328921378-118.13181343256.8328740616-68.3013364745
502.99285144561-0.0708008659336-0.5978840412743.422550855610.9752122647742.939593421230.2942060253270.519257378384-0.404661981603-0.855808879443-0.1779992414970.124496763676-0.5166071579890.039529135259-0.06425581405431.939963554250.0624356694402-0.4445698355060.956099256425-0.08707829819561.2069570727-109.52792677356.0608466012-71.0846821565
512.409098099550.6916867215250.609455438172.230822474420.1170058400262.79158609415-0.305818500811-0.1171410583660.01684399961060.4742979756590.268238779481-0.403028558005-0.3599396790910.396651445971-0.07810197065981.498953019150.0384095752019-0.02957442337441.002192799680.04867605145441.02214021303-126.358584966.7760934306212.2028025552
523.800786967370.979252490246-0.7581645986254.51058004921-1.355738538333.72610547917-0.0301453690761-0.452677140949-0.1858605312110.556392990857-0.1310380250460.717844348189-0.1075894675850.0872625520045-0.02695249479521.354631200750.04630576217970.22533666640.9809121767170.1625532461091.17361677951-147.754819032-4.420126239978.90120189537
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 819 )AA720 - 819406 - 505
44chain 'A' and (resid 820 through 963 )AA820 - 963506 - 649
55chain 'A' and (resid 964 through 1061 )AA964 - 1061650 - 747
66chain 'A' and (resid 1062 through 1140 )AA1062 - 1140748 - 826
77chain 'B' and (resid 715 through 832 )BC715 - 8321 - 118
88chain 'B' and (resid 833 through 880 )BC833 - 880119 - 166
99chain 'B' and (resid 881 through 914 )BC881 - 914167 - 200
1010chain 'B' and (resid 915 through 1026 )BC915 - 1026201 - 312
1111chain 'B' and (resid 1027 through 1041 )BC1027 - 1041313 - 327
1212chain 'C' and (resid 20 through 42 )CE20 - 421 - 23
1313chain 'C' and (resid 43 through 64 )CE43 - 6424 - 45
1414chain 'C' and (resid 65 through 123 )CE65 - 12346 - 104
1515chain 'C' and (resid 124 through 150 )CE124 - 150105 - 131
1616chain 'C' and (resid 151 through 174 )CE151 - 174132 - 155
1717chain 'C' and (resid 175 through 218 )CE175 - 218156 - 199
1818chain 'C' and (resid 219 through 243 )CE219 - 243200 - 224
1919chain 'C' and (resid 244 through 267 )CE244 - 267225 - 248
2020chain 'D' and (resid 1 through 353 )DH1 - 3531 - 353
2121chain 'D' and (resid 354 through 819 )DH354 - 819354 - 506
2222chain 'D' and (resid 820 through 1140 )DH820 - 1140507 - 827
2323chain 'F' and (resid 20 through 42 )FJ20 - 421 - 23
2424chain 'F' and (resid 43 through 63 )FJ43 - 6324 - 44
2525chain 'F' and (resid 64 through 106 )FJ64 - 10645 - 87
2626chain 'F' and (resid 107 through 135 )FJ107 - 13588 - 116
2727chain 'F' and (resid 136 through 150 )FJ136 - 150117 - 131
2828chain 'F' and (resid 151 through 174 )FJ151 - 174132 - 155
2929chain 'F' and (resid 175 through 217 )FJ175 - 217156 - 198
3030chain 'F' and (resid 218 through 243 )FJ218 - 243199 - 224
3131chain 'F' and (resid 244 through 267 )FJ244 - 267225 - 248
3232chain 'G' and (resid 1 through 129 )GM1 - 1291 - 129
3333chain 'G' and (resid 130 through 307 )GM130 - 307130 - 307
3434chain 'G' and (resid 308 through 743 )GM308 - 743308 - 429
3535chain 'G' and (resid 744 through 795 )GM744 - 795430 - 481
3636chain 'G' and (resid 796 through 1140 )GM796 - 1140482 - 826
3737chain 'I' and (resid 20 through 42 )IO20 - 421 - 23
3838chain 'I' and (resid 43 through 123 )IO43 - 12324 - 104
3939chain 'I' and (resid 124 through 150 )IO124 - 150105 - 131
4040chain 'I' and (resid 151 through 174 )IO151 - 174132 - 155
4141chain 'I' and (resid 175 through 218 )IO175 - 218156 - 199
4242chain 'I' and (resid 219 through 233 )IO219 - 233200 - 214
4343chain 'I' and (resid 234 through 243 )IO234 - 243215 - 224
4444chain 'I' and (resid 244 through 267 )IO244 - 267225 - 248
4545chain 'E' and (resid 715 through 768 )EP715 - 7681 - 54
4646chain 'E' and (resid 769 through 794 )EP769 - 79455 - 80
4747chain 'E' and (resid 795 through 872 )EP795 - 87281 - 158
4848chain 'E' and (resid 873 through 901 )EP873 - 901159 - 187
4949chain 'E' and (resid 902 through 931 )EP902 - 931188 - 217
5050chain 'E' and (resid 932 through 1043 )EP932 - 1043218 - 329
5151chain 'H' and (resid 715 through 880 )HR715 - 8801 - 166
5252chain 'H' and (resid 881 through 1044 )HR881 - 1044167 - 330

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  • 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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