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- PDB-8buq: Structure of DDB1 bound to DS43-engaged CDK12-cyclin K -

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Basic information

Entry
Database: PDB / ID: 8buq
TitleStructure of DDB1 bound to DS43-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 / host-mediated suppression of viral genome replication / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity ...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 / host-mediated suppression of viral genome replication / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / positive regulation by virus of viral protein levels in host cell / negative regulation of stem cell differentiation / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / cyclin-dependent protein serine/threonine kinase activator activity / UV-damage excision repair / [RNA-polymerase]-subunit kinase / positive regulation of DNA-templated transcription, elongation / regulation of cyclin-dependent protein serine/threonine kinase activity / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ectopic germ cell programmed cell death / regulation of signal transduction / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / proteasomal protein catabolic process / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of gluconeogenesis / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / RNA splicing / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / mRNA processing / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / protein autophosphorylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transcription by RNA polymerase II / chromosome, telomeric region / protein kinase activity / nuclear speck / protein ubiquitination / cell division / protein serine kinase activity / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / protein kinase binding / nucleolus / 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 / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region ...Cyclin-T2-like, C-terminal domain / DNA polymerase; domain 1 - #910 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-RQ9 / 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: 3.2 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)499,07518
Polymers496,5589
Non-polymers2,5189
Water00
1
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,3586
Polymers165,5193
Non-polymers8393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,3586
Polymers165,5193
Non-polymers8393
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)166,3586
Polymers165,5193
Non-polymers8393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.162, 250.162, 218.849
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 1015 or resid 1020 through 1140))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1015 or resid 1020 through 1140))
d_1ens_2(chain "B" and resid 715 through 1027)
d_2ens_2(chain "E" and (resid 715 through 796 or resid 801 through 1027))
d_3ens_2(chain "H" and (resid 715 through 796 or resid 801 through 1027))
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLYGLYAA1 - 3935 - 397
d_12ens_1LYSLYSHISHISAA709 - 1140409 - 840
d_21ens_1METMETGLYGLYDD1 - 3935 - 397
d_22ens_1LYSLYSHISHISDD709 - 1140409 - 840
d_31ens_1METMETGLYGLYGG1 - 3935 - 397
d_32ens_1LYSLYSHISHISGG709 - 1140409 - 840
d_11ens_2THRTHRLYSLYSBB715 - 10277 - 319
d_12ens_2RQ9RQ9RQ9RQ9BK1101
d_21ens_2THRTHRLYSLYSEE715 - 10277 - 319
d_22ens_2RQ9RQ9RQ9RQ9EN1101
d_31ens_2THRTHRLYSLYSHH715 - 10277 - 319
d_32ens_2RQ9RQ9RQ9RQ9HP1101
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(-0.474369687863, -0.515733781056, 0.713436799103), (0.508527911192, 0.500995977612, 0.700287365269), (-0.718590817347, 0.694997624093, 0.0246077168915)-127.418077367, 80.0574492374, -108.519782716
2given(-0.518764067027, 0.501635800118, -0.692275499206), (-0.546693024757, 0.427905465113, 0.71973859811), (0.657275117013, 0.751836708978, 0.0522588135078)-180.0101681, -28.619248572, 33.9866325653
3given(-0.504266933748, -0.517330383134, 0.691436283554), (0.501598945885, 0.476293641536, 0.722179246807), (-0.702931971826, 0.710994825381, 0.0193132406736)-129.153930935, 79.8104322734, -107.597463197
4given(-0.513439519537, 0.503468763224, -0.694909392824), (-0.54276681097, 0.436702144323, 0.717422766612), (0.664668374972, 0.74552695565, 0.0490459958766)-179.800646124, -28.5010206035, 34.2404492635
5given(-0.557665041078, -0.512701324379, 0.652799397931), (0.47935919449, 0.443129369586, 0.757529619532), (-0.677661024862, 0.73537317995, -0.00134966422462)-133.199414018, 80.2920541761, -107.318022725
6given(-0.489042538698, 0.525207046971, -0.696415790428), (-0.520373902622, 0.465089948872, 0.716172005127), (0.7000345683, 0.712635178244, 0.0458552713971)-179.395973784, -28.2662843311, 37.2558253166

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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


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-RQ9 / (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol


Mass: 454.956 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H27ClN8O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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, Jeff600 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: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.199→216.647 Å / Num. obs: 105078 / % possible obs: 96.4 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 3.199→3.393 Å / Num. unique obs: 5252 / CC1/2: 0.463

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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: 3.2→54.3 Å / SU ML: 0.3245 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 5174 4.93 %
Rwork0.195 99837 -
obs0.196 105011 80.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.21 Å2
Refinement stepCycle: LAST / Resolution: 3.2→54.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33402 0 174 0 33576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002834268
X-RAY DIFFRACTIONf_angle_d0.626246328
X-RAY DIFFRACTIONf_chiral_restr0.04545134
X-RAY DIFFRACTIONf_plane_restr0.00375941
X-RAY DIFFRACTIONf_dihedral_angle_d11.740112888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.986166870798
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.05820581133
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.875007947354
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.785732480904
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.681554737783
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.546090769237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.230.521950.3699115X-RAY DIFFRACTION2.82
3.23-3.270.424220.3583537X-RAY DIFFRACTION13.09
3.27-3.310.3059560.35721114X-RAY DIFFRACTION27.24
3.31-3.350.3271750.33491653X-RAY DIFFRACTION39.89
3.35-3.40.321840.32091881X-RAY DIFFRACTION46.05
3.4-3.450.30551110.30562189X-RAY DIFFRACTION53.65
3.45-3.490.2991360.30022473X-RAY DIFFRACTION60.14
3.49-3.550.30251290.28562656X-RAY DIFFRACTION65.18
3.55-3.60.3071660.28242885X-RAY DIFFRACTION70.84
3.6-3.660.28241380.27023199X-RAY DIFFRACTION77.33
3.66-3.720.27241690.27263333X-RAY DIFFRACTION81.57
3.72-3.790.28571900.25963609X-RAY DIFFRACTION86.97
3.79-3.860.26842170.25933784X-RAY DIFFRACTION93.79
3.87-3.940.26292040.25514062X-RAY DIFFRACTION98.57
3.94-4.030.24552380.23814091X-RAY DIFFRACTION99.95
4.03-4.120.222050.22614102X-RAY DIFFRACTION100
4.12-4.230.24262010.20784120X-RAY DIFFRACTION100
4.23-4.340.21031970.19524137X-RAY DIFFRACTION100
4.34-4.470.20962260.18634111X-RAY DIFFRACTION100
4.47-4.610.19942220.18044103X-RAY DIFFRACTION100
4.61-4.780.2122280.17674081X-RAY DIFFRACTION100
4.78-4.970.19732220.17764139X-RAY DIFFRACTION100
4.97-5.190.2152270.18254128X-RAY DIFFRACTION99.98
5.19-5.470.23041570.19084178X-RAY DIFFRACTION100
5.47-5.810.2222110.19714165X-RAY DIFFRACTION100
5.81-6.260.22892320.19644129X-RAY DIFFRACTION100
6.26-6.890.25442240.19584149X-RAY DIFFRACTION100
6.89-7.880.19852370.18014170X-RAY DIFFRACTION100
7.88-9.920.1542390.14264200X-RAY DIFFRACTION100
9.92-54.30.17412060.15754344X-RAY DIFFRACTION99.37
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)
11.576192975280.669093800716-0.2558078509581.25001493998-0.1155080481171.37519190238-0.0840457585594-0.320651050677-0.2158838596160.4380182666510.0365891804613-0.3424983018090.2189345225780.4253459198790.02449647676321.236320211010.164599770404-0.3328122379231.110497676050.01713890180921.26328499564-57.5767335652-7.7173851312327.8454991961
20.6438609169840.330789066202-0.6998951460322.80172277519-0.2451211330080.3249154691760.0529336352036-0.6111772878470.219905408640.740118555082-0.103101647753-0.370292121756-0.0821419314380.1810798770440.02309939062881.38475002119-0.0768792716454-0.218236949391.26626178342-0.1389948480581.06355832194-73.423586214810.055082001239.6896149253
31.84621099957-0.424894660527-0.2370011986973.15844773982-1.111813268760.9917824413430.0778888315059-0.0426559603462-0.005546221437030.144238042171-0.06109294887070.291033784679-0.0878796144134-0.140235243730.03363558824381.10764854566-0.0585370256463-0.07695199185760.877780368924-0.1157019230120.959349026233-89.081226888718.839156824722.6602511741
41.98752086124-0.3781663986760.1500253622590.702236635396-0.2592838534641.791676819960.152294524031-0.04283915935630.3911188055940.1409834906940.00322169326957-0.440768663054-0.3403220332240.4337272375690.1021137066451.16325076955-0.157561364232-0.1471633763840.917403431733-0.2308611891341.22341135955-60.291656031729.569313656521.5181808972
50.8827940107310.0753043029367-1.52816724671.98007216028-1.169537503253.85501435453-0.03347847549920.0159615455091.302022513250.05285275323830.0930301864146-0.310748579797-0.9400426823690.1990558008610.0351933721471.2190966465-0.00807401241283-0.06616195936111.138815623670.02403801278951.39016622919-65.652012064634.3944999209-13.5265109633
61.48008006095-0.369595284103-1.195643096021.81593343476-0.5136799723462.065394647570.1361660393070.2137492863980.3696439403570.128974464490.0381535307615-0.15514872692-0.7828132296870.04249088202830.02234098859581.22902737963-0.106833582032-0.07488700536560.941552740626-0.1776775509711.13233085533-60.471174868730.10060627-15.5199657919
72.276513409350.3052178273240.008285939136642.2524355929-0.6949468438171.30840922436-0.156988217054-0.5728340005560.3474277618120.5086716347310.3490724689830.456500875102-0.7086646034150.018267519323-0.03601801697631.52654112770.007454822499320.04285501741531.25505942233-0.1693040938561.17801864974-61.997474131227.7397866702-7.37203656376
81.188282578130.16091419761-0.03937766277812.69868816877-0.5787922663332.444824490290.0796514470538-0.0580079024848-0.311764736987-0.361620095092-0.169871567190.15241622053-0.246044058577-0.1452776963340.001244792226341.12625254568-0.0726351127810.09148206627240.934821626386-0.2315945097511.29230069096-57.223570711112.6118564223-12.2506520522
90.1814885697910.336346916391-0.09390807379540.56310233259-0.1556693448970.0259099481121.011884031610.2050306478570.0684216128856-0.922204492257-0.340341597936-1.615490040511.18899391152.532919453060.001129729607811.79053414267-0.0650549329260.306129518552.133418478480.002521452536992.24942073501-41.05286857818.3045055527-15.7898776939
102.95509354036-1.336284878-1.011028754852.71300464551-0.1154164773792.09281963472-0.131360790689-0.0374257711380.1698140002450.1434253188940.0742649041653-0.6328574272560.001610040694860.7719850041250.03315089857381.1334208686-0.0336575536671-0.0946969035631.26195445412-0.2573275495081.49635639313-41.26392066955.38116721266-5.5309100202
110.103730458335-0.174717561815-0.09365797731830.09674599369470.1799864054650.08746420949230.2325178669210.2562376640810.109594014267-0.640917519296-0.566914429814-0.11208174532-0.922192006908-0.3352625342750.1976862827251.78806710687-0.126007279314-0.1221642377271.85881150282-0.5748747982112.33947521022-69.8014170896.3015571511-2.51970914643
122.24547420613-0.1574575621510.9109612708214.91465963144-0.2564762977292.346547363270.2375026744520.1923457514450.2005210191530.423808545923-0.1912112577770.3499755760190.003045741124240.251173113594-0.08856049936731.14805658029-0.09307007038210.1987526826751.05456155935-0.1093182387420.996330777824-61.225489814240.6475993465-42.389493916
131.27479362043-1.243814503931.657015691661.56162329046-1.359195790472.824881082910.2729995007850.2191959967020.597909198345-0.928051954790.174405979546-1.131526847290.1716330514640.9416770504920.06997578926651.12982853712-0.3493732592570.1924516301171.28204596877-0.3419615008931.46589111441-44.03762847343.6824977686-40.9629035849
141.839120164981.08107514714-1.024121482262.13442159336-0.9700676494652.140824705650.0882298913449-0.2548102828940.4651533024140.5788610051690.0105024893467-0.470013549594-0.4316644850060.4294968431670.02208970100531.08660814692-0.13915966514-0.0324051669080.948445345628-0.2209689010291.3112623628-46.106188833943.2507031083-29.622629559
150.542791390451-1.07752608578-0.3429900201152.527366614290.562860768371.27951331655-0.198184843155-0.292886081362-0.5599904703220.1678466551750.0275752935659-0.6532141280810.1517124184770.3639484212390.02393344510421.00530113234-0.05032572293180.1567386105340.962503500311-0.1782833897851.35894164564-45.922640082724.2239393493-44.9568731862
161.35130149321-1.134976955270.599958337313.647081674770.7321210564241.44482026673-0.3711461302170.53021157055-0.0848416792975-0.5118197082660.452564662731-0.0224066664954-0.357764181137-0.1947366641780.05489289968771.278243702790.0219537027789-0.008781457994491.13121486848-0.2789936056191.60741958564-50.293478103413.2372926976-54.3701237103
170.765307877070.144091416948-1.092856119254.2939679259-0.8825334055272.20021801437-0.5592314688361.510637744851.49165452714-0.5692322489960.0136796885686-1.57943992253-0.8334729076310.288618886098-0.004414724964151.45945586428-0.0974770105259-0.0011654379861.102888737180.1151504332641.62355057259-45.573259444133.1250274334-55.2790828477
182.43086880669-0.3831842676030.202118579690.749218635076-0.0522611605491.19497511171-0.1027869840080.4471139127240.114499174269-0.5456724125410.125778499796-0.0925887710887-0.2434740742340.248960851089-0.01488771323931.60134091924-0.2576406568990.1011045497761.042201773630.01156154980960.904818701651-76.273996757566.3944258459-71.8433219847
191.42394268184-0.432127695205-0.5986151497350.699375835435-0.1904187444281.82538692087-0.175442885882-0.1426864806590.256401422812-0.2644063950350.131982806923-0.487395136563-0.4793499222220.359966899469-0.0718818969191.08213735909-0.246591984955-0.06355708616130.803639508157-0.1501970729091.01167484064-70.632231596972.0391543302-43.8404081701
202.409354306780.6971994448430.405386773421.4767266276-0.2237547114392.537564178420.00246428037508-0.445577423517-0.12957412445-0.0308305914895-0.0379455774506-0.07973237975890.0564202224515-0.07509175710220.006975628162320.793002918413-0.133926683842-0.08412413269940.734946486943-0.1210621924330.627176891792-86.81657539360.3529886427-28.2818064553
211.104551421550.307534143452-0.2148463721791.09179362668-0.9466568598722.29123133967-0.07950537739380.1737167587060.470329544343-0.3164411211220.03994727653480.226714595316-0.795978280441-0.572117423088-0.09863177026541.472824500440.0710099993068-0.1806556371510.87649152393-0.1146307977221.17357830697-99.400495383984.3323816752-48.8184013851
224.582058371131.180048077311.365856205340.2512668375350.07085890051131.900102107680.0802720008273-0.672981818555-0.3793087491230.2183642984510.1414744771310.1752735807110.3359580273790.133864031972-0.01500542960190.9963252760990.0507116256667-0.1418903270580.969267969177-0.1392345551861.19636893525-123.77936886355.3384387059-38.4038077517
232.753103897510.972795110523-0.9490934682231.642423384810.4284966536671.25834212221-0.220411654819-0.578631983643-0.135200952969-0.284792877127-0.0996104422511-0.0023766215885-0.2671895334020.181844914707-0.02215087219661.0771565281-0.0114331203365-0.1256789193431.22340016923-0.1096789589190.98524667348-126.59939683452.3214587058-42.6431259608
241.294533816780.726256714093-1.30379048233.912661264060.5985339765125.049830951350.09514296023730.3488736001560.300904173471-0.361041163937-0.04404202663770.317590555652-0.683895657864-0.263141422696-0.01518746871131.191676638750.0982058548966-0.3399131416580.885871039172-0.1400804590791.01773856346-117.51409612153.1629688478-62.6456568903
253.84827582274-0.00031828232534-1.065800763783.258565627291.582564842423.264115362470.08618127278220.399467233612-0.00978747501886-1.060487164710.04303051541190.0201402990308-0.806476290393-0.37670905358-0.003461188436291.669527403780.0760653836616-0.3767001079850.907330790121-0.09123993938340.844604790083-113.0985048956.3217861433-75.7452229125
262.538018353520.776365206921-0.5068256072292.465768867380.1498807993933.0006738748-0.198074696052-0.0645425481992-0.2169355685950.07664757183930.0513379275130.2354451046610.0778311350816-0.338127363168-0.05215454704820.7596026734390.0792085042505-0.2021939969880.658702106418-0.01000421476940.856852830927-150.31924667445.8199523467-42.4205231344
272.82821690433-0.1769016200870.7233933401833.20725026662-0.1653820395242.00439228578-0.2499843291090.05006997664060.8747006689730.006790558123110.135764242024-0.533644848771-0.887575763209-0.207072236725-0.04933719406791.180333956920.112760839136-0.06168696482940.871434172549-0.06861095719130.947856789629-150.02844697259.9143250136-43.8555800268
281.07986237412-0.121426671019-0.1633662318062.402034829141.287954434013.02606008751-0.03379004184690.296542410928-0.0700788074716-0.04783421934750.0437303388355-0.2520843966430.3538318520140.122134963993-0.04946857308050.8234625068770.0613056248605-0.08327632542940.777396386544-0.0281562582660.917887275716-149.11969340935.0331265055-58.2564239226
290.425978575935-0.850776043485-0.5035512080221.72551968521.258271782861.868976722320.03097661776210.319751763655-0.2770253404610.175470852536-0.2223477179560.1168641816540.6372696189650.166393373065-0.1133325414751.195587757090.168618882178-0.05610311593670.881927984603-0.04094592204321.1283484496-147.90417093221.0474996706-63.5358434107
303.68111737503-0.461905010501-2.265812048652.763175527312.327686447023.926310557880.349928060673-0.448187631159-0.6662521242731.19653342593-0.06974720803731.13179694142-0.0952846176887-1.71572513422-0.09968747599861.08881102207-0.008087286053970.04139904405291.33532757231-0.008977132796381.11826258799-160.73870731231.383870569-51.9022518291
310.953974481751-0.1076748439790.1091098312821.98193358784-0.2895382695182.23660684765-0.170512901769-0.0127429126139-0.150031851464-0.1946735805810.1034554305530.95020622964-0.0473121849404-0.442453685246-0.01800986290881.101113380370.10710521874-0.08045369379771.088615077480.03530348362741.47960139584-173.27664234619.0932270262-7.36133337312
322.053395789510.7639491860090.2807283476742.00171154666-0.09020777779181.94250842058-0.08332526069610.08810047265870.3641139179120.1839643780110.1068055204340.278989351573-0.470100834988-0.1410485765440.003419915142721.340028106640.240341251211-0.07760945488490.6785025831810.04056898118971.04592610881-156.34249458743.0172849875-9.71682750881
331.849933124070.0133074487357-0.1123478892152.02238537492-0.3224711381060.926912807564-0.222516298693-0.4750636746720.1736024360320.7690837927680.08852699653850.0347602620566-0.433578500908-0.0971707146057-0.06759529234411.55795370590.1547021711310.01128722277940.833527946259-0.09816327706650.94264124259-146.78031694335.089393522813.8528137108
341.52916070787-0.751292999571.502813194924.19968525571-2.453612248132.28311523107-0.211285896084-0.2769762479670.2582183234120.3842449604620.397599828278-0.5371107900760.04789160268550.489219132998-0.01407780281451.290698944790.0965963652265-0.1005684106170.872094184936-0.04112579924441.06776505303-120.85495327512.163225605617.0935268238
352.939670716170.3114129119291.575339638722.751378262230.5027895451742.3803891866-0.201701260348-0.02479588731060.304697610942-0.08979851937790.101091574553-0.324178488853-0.1651842681410.1252668812520.04313026503660.864505422839-0.04769678512140.09889182362540.618052753307-0.01975643847240.742970598046-129.6251998044.075047886910.0099936337
362.548684880840.571064646857-0.1553617011880.8808381933731.654139654673.670115891370.182466445284-0.620774110455-0.8575914285190.731885807892-0.1650195881490.05011693509940.4653391764690.0310974977760.08265815969881.29528057504-0.0902505550861-0.06618452327410.994105585970.1367654359681.23055184506-133.180557405-9.5456190192516.8108575987
372.093006951210.5416976031420.7304277931225.07713719049-0.7696633724762.35576997127-0.0288328053805-0.144384056414-0.1423800007980.160831675756-0.03672259354450.5555210641-0.213210924365-0.172687790144-0.0369808213740.8470920482490.01833730658760.1007533616680.6345894048940.03045629516570.770695652332-150.22317915-6.019566742529.15437117734
383.944780415721.002352982411.127290131071.910817734070.5748388058673.29925288841-0.3815984137280.439961064302-0.293633327736-0.1850864166840.0471382169437-0.139609333890.09492537246410.06949394256450.0404986930181.25185924728-0.00120855919896-0.08322960522670.927043986280.01330600400991.05853641369-98.6066150587-7.8668933900821.3787657963
396.009429769540.335240962101-0.1439938110471.411070576950.2859459670140.622223347423-0.424739757-0.740683598304-1.602178444580.5799892124760.1918226670470.1402613455250.6911040467890.5012806924590.06735514743631.420000499460.1700240427960.01764044132890.7476965232910.08767526635620.926099667484-106.443905769-14.344785583335.7460872917
402.92209760714-0.4377370787550.523526705942.16397047946-0.8615864521542.12284538866-0.0658321211724-0.6505066457410.1608484568190.510375305971-0.1930854863610.135833671268-0.343221814032-0.2134862129480.003772931823411.25384326292-0.003354057077160.08534514511520.90282619266-0.1030640570920.690979169256-113.49756749-5.4279050075734.4327314565
411.639229123680.06056871817360.05694098573232.531793228161.353120711851.3999856915-0.2626216749090.0973536200485-0.183771675393-0.09953473790180.1013801461670.4854377918710.241305308452-0.4065342736120.01036981161981.08081992529-0.06550770431980.1262461379140.6909556204920.01508325541670.836873307855-112.903604473-25.280050142120.3047369367
422.215584235941.019676408190.323834168262.060023822821.214632177172.17301336884-0.1478362698850.330663404417-0.443052704104-0.2503658488560.337949908075-0.09386787214820.6347378290510.4212795726120.04190826702361.36211926233-0.005150722338480.2662401747110.906780031298-0.0628974644830.983480565559-110.051177291-34.80687129869.02177286511
432.91006071480.3365536034642.535920674084.15267709250.8058843935854.577646184830.654303820491-1.42267629807-0.7383594653211.38321149491-0.246510696793-1.844973056451.069949622510.919886924930.1539385128311.491041020060.0471947534898-0.1175542214281.073134142450.2108465986361.25407843477-101.107892039-28.676074539926.4395860886
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 - 822
55chain 'B' and (resid 715 through 740 )BC715 - 7401 - 26
66chain 'B' and (resid 741 through 794 )BC741 - 79427 - 80
77chain 'B' and (resid 795 through 832 )BC795 - 83281 - 114
88chain 'B' and (resid 833 through 880 )BC833 - 880115 - 162
99chain 'B' and (resid 881 through 901 )BC881 - 901163 - 183
1010chain 'B' and (resid 902 through 1020 )BC902 - 1020184 - 302
1111chain 'B' and (resid 1021 through 1039 )BC1021 - 1039303 - 321
1212chain 'C' and (resid 20 through 42 )CE20 - 421 - 23
1313chain 'C' and (resid 43 through 63 )CE43 - 6324 - 44
1414chain 'C' and (resid 64 through 150 )CE64 - 15045 - 131
1515chain 'C' and (resid 151 through 218 )CE151 - 218132 - 199
1616chain 'C' and (resid 219 through 243 )CE219 - 243200 - 224
1717chain 'C' and (resid 244 through 267 )CE244 - 267225 - 248
1818chain 'D' and (resid 1 through 307 )DG1 - 3071 - 307
1919chain 'D' and (resid 308 through 761 )DG308 - 761308 - 448
2020chain 'D' and (resid 762 through 917 )DG762 - 917449 - 604
2121chain 'D' and (resid 918 through 1140 )DG918 - 1140605 - 827
2222chain 'E' and (resid 715 through 768 )EI715 - 7681 - 54
2323chain 'E' and (resid 769 through 819 )EI769 - 81955 - 105
2424chain 'E' and (resid 820 through 931 )EI820 - 931106 - 217
2525chain 'E' and (resid 932 through 1027 )EI932 - 1027218 - 313
2626chain 'F' and (resid 20 through 106 )FK20 - 1061 - 87
2727chain 'F' and (resid 107 through 150 )FK107 - 15088 - 131
2828chain 'F' and (resid 151 through 217 )FK151 - 217132 - 198
2929chain 'F' and (resid 218 through 243 )FK218 - 243199 - 224
3030chain 'F' and (resid 244 through 267 )FK244 - 267225 - 248
3131chain 'G' and (resid 1 through 294 )GM1 - 2941 - 294
3232chain 'G' and (resid 295 through 795 )GM295 - 795295 - 481
3333chain 'G' and (resid 796 through 1140 )GM796 - 1140482 - 826
3434chain 'H' and (resid 715 through 768 )HN715 - 7681 - 54
3535chain 'H' and (resid 769 through 872 )HN769 - 87255 - 158
3636chain 'H' and (resid 873 through 892 )HN873 - 892159 - 178
3737chain 'H' and (resid 894 through 1035 )HN894 - 1035180 - 321
3838chain 'I' and (resid 20 through 42 )IQ20 - 421 - 23
3939chain 'I' and (resid 43 through 63 )IQ43 - 6324 - 44
4040chain 'I' and (resid 64 through 150 )IQ64 - 15045 - 131
4141chain 'I' and (resid 151 through 218 )IQ151 - 218132 - 199
4242chain 'I' and (resid 219 through 243 )IQ219 - 243200 - 224
4343chain 'I' and (resid 244 through 267 )IQ244 - 267225 - 248

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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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