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- PDB-8bua: Structure of DDB1 bound to 919278-engaged CDK12-cyclin K -

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Basic information

Entry
Database: PDB / ID: 8bua
TitleStructure of DDB1 bound to 919278-engaged CDK12-cyclin K
Components
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
KeywordsLIGASE / kinase / cyclin / ubiquitin / degrader
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / negative regulation of stem cell differentiation / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / viral release from host cell / regulation of signal transduction / ectopic germ cell programmed cell death / proteasomal protein catabolic process / cyclin-dependent kinase / positive regulation of viral genome replication / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of gluconeogenesis / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / RNA splicing / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA processing / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein autophosphorylation / chromosome, telomeric region / damaged DNA binding / protein kinase activity / protein ubiquitination / nuclear speck / cell cycle / cell division / DNA repair / protein serine kinase activity / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Cyclin, N-terminal ...Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin, C-terminal domain / Cyclin_C / Cyclin/Cyclin-like subunit Ssn8 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Chem-RVH / 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: 3.193 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)499,24821
Polymers496,5589
Non-polymers2,69012
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)166,2246
Polymers165,5193
Non-polymers7053
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)166,4167
Polymers165,5193
Non-polymers8974
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)166,6088
Polymers165,5193
Non-polymers1,0895
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.329, 250.329, 217.561
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 or resid 1201))
d_2ens_1(chain "D" and (resid 1 through 393 or resid 709 through 1140 or resid 1201))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1140 or resid 1201))
d_1ens_2(chain "B" and (resid 715 through 1033 or resid 1101))
d_2ens_2chain "E"
d_3ens_2(chain "H" and (resid 715 through 1033 or resid 1101))
d_1ens_3chain "C"
d_2ens_3(chain "F" and (resid 20 through 267 or resid 301))
d_3ens_3(chain "I" and (resid 20 through 267 or resid 301))

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_13ens_1CITCITCITCITAJ1201
d_21ens_1METMETGLYGLYDD1 - 3935 - 397
d_22ens_1LYSLYSHISHISDD709 - 1140409 - 840
d_23ens_1CITCITCITCITDM1201
d_31ens_1METMETGLYGLYGG1 - 3935 - 397
d_32ens_1LYSLYSHISHISGG709 - 1140409 - 840
d_33ens_1CITCITCITCITGQ1201
d_11ens_2THRTHRASPASPBB715 - 10327 - 324
d_12ens_2RVHRVHRVHRVHBK1101
d_21ens_2THRTHRASPASPEE715 - 10327 - 324
d_22ens_2RVHRVHRVHRVHEN1101
d_31ens_2THRTHRASPASPHH715 - 10327 - 324
d_32ens_2RVHRVHRVHRVHHR1101
d_11ens_3THRTHRHISHISCC20 - 26724 - 271
d_12ens_3CITCITCITCITCL301
d_21ens_3THRTHRHISHISFF20 - 26724 - 271
d_22ens_3CITCITCITCITFO301
d_23ens_3CITCITCITCITFP302
d_31ens_3THRTHRHISHISII20 - 26724 - 271
d_32ens_3CITCITCITCITIT301
d_33ens_3CITCITCITCITIU302

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.464550764245, -0.513081785187, 0.721761504341), (0.505192646196, 0.515851609714, 0.69186523759), (-0.727305285055, 0.686035129177, 0.0195658852442)-126.88015335, 79.7272233681, -109.202640595
2given(-0.521375445576, 0.497260246073, -0.693469460341), (-0.545548430273, 0.430653152448, 0.718967852211), (0.656158940332, 0.753173359833, 0.0467475674357)-179.815222426, -28.6999762296, 34.0646227949
3given(-0.49253576718, -0.519547955416, 0.698196562632), (0.501018030103, 0.486706295849, 0.71561016978), (-0.711610463358, 0.702272670409, 0.0205826343489)-128.436019482, 79.713519646, -108.364656655
4given(-0.52294176813, 0.500048981067, -0.690277425155), (-0.53362376356, 0.439432143215, 0.722596063146), (0.664663513448, 0.746224100417, 0.0370405972956)-180.188028147, -28.2096178011, 34.349606379
5given(-0.578158831169, -0.500710846817, 0.644221246018), (0.464318598398, 0.447339649804, 0.764392227129), (-0.670925185936, 0.741064022601, -0.0261440104689)-135.167361269, 79.6726635205, -108.077725761
6given(-0.481014221568, 0.519831929713, -0.705974562928), (-0.522331543311, 0.476810565954, 0.706980511087), (0.704127174246, 0.708820463196, 0.0421719508916)-179.065755894, -29.1667111706, 37.8966496027

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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.: 9 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-RVH / (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide


Mass: 320.345 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H16N4O2 / 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, 100 %w/v SB38D2, 0.07 M 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: 3.193→216.791 Å / Num. obs: 112997 / % possible obs: 96.5 % / Redundancy: 21.1 % / CC1/2: 0.999 / Net I/σ(I): 14.9
Reflection shellResolution: 3.245→3.361 Å / Num. unique obs: 5648 / 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: 3.193→72.52 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6561
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2245 5520 4.89 %
Rwork0.2006 107427 -
obs0.2018 112947 86.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.01 Å2
Refinement stepCycle: LAST / Resolution: 3.193→72.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33494 0 189 0 33683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005634375
X-RAY DIFFRACTIONf_angle_d0.909746483
X-RAY DIFFRACTIONf_chiral_restr0.05385146
X-RAY DIFFRACTIONf_plane_restr0.0065977
X-RAY DIFFRACTIONf_dihedral_angle_d13.141312925
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.04138987143
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.71217997036
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.14218591721
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.957883228596
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.882858259134
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.815042563333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.193-3.230.352180.4734332X-RAY DIFFRACTION8.21
3.23-3.270.465320.4452896X-RAY DIFFRACTION21.7
3.27-3.310.4238670.4011504X-RAY DIFFRACTION36.35
3.31-3.350.3696910.3742026X-RAY DIFFRACTION48.98
3.35-3.390.32641170.34882522X-RAY DIFFRACTION61.52
3.39-3.440.30911280.32332866X-RAY DIFFRACTION69.86
3.44-3.490.30231760.30643259X-RAY DIFFRACTION79.28
3.49-3.540.26461680.28953444X-RAY DIFFRACTION84.49
3.54-3.60.30362110.28423764X-RAY DIFFRACTION91.97
3.6-3.660.33281830.27774021X-RAY DIFFRACTION97.72
3.66-3.720.30212150.28344105X-RAY DIFFRACTION99.86
3.72-3.790.30212080.29074089X-RAY DIFFRACTION100
3.79-3.860.31032340.28874117X-RAY DIFFRACTION100
3.86-3.940.29261980.26554097X-RAY DIFFRACTION100
3.94-4.020.25812420.23994086X-RAY DIFFRACTION100
4.02-4.120.22262000.22194113X-RAY DIFFRACTION100
4.12-4.220.22672100.20434116X-RAY DIFFRACTION100
4.22-4.330.2221890.19494152X-RAY DIFFRACTION100
4.33-4.460.22032280.19434083X-RAY DIFFRACTION100
4.46-4.60.19942180.18984134X-RAY DIFFRACTION100
4.61-4.770.2132320.19334094X-RAY DIFFRACTION100
4.77-4.960.19972240.17984135X-RAY DIFFRACTION100
4.96-5.190.20752290.18214107X-RAY DIFFRACTION100
5.19-5.460.20741550.18824212X-RAY DIFFRACTION100
5.46-5.80.23662110.20184135X-RAY DIFFRACTION100
5.8-6.250.22772320.19984153X-RAY DIFFRACTION100
6.25-6.880.24332240.1884148X-RAY DIFFRACTION100
6.88-7.870.22422350.18054165X-RAY DIFFRACTION100
7.87-9.910.16092410.13414210X-RAY DIFFRACTION100
9.91-72.520.17192040.14584342X-RAY DIFFRACTION99.13
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)
11.37607339892-0.156338426159-0.2330672365851.31216737625-0.01241144770290.962248155264-0.0431622731639-0.349545000408-0.1839995866980.4476249787230.0266458997282-0.2758172518630.1761106250750.337311364134-0.01347515325731.108938813680.0831336328336-0.2811004223141.03745385783-0.03904930978791.04500344405-61.0499286294-3.52704985930.7455973018
21.8823621875-0.262494218597-0.08832216370973.99398150658-1.715100307131.126297615140.0671315883156-0.04267253816690.03304350032970.03292115219040.02804336056920.235871543826-0.152630227381-0.1021283464170.004832542427450.932538177268-0.0435344587433-0.02334410053620.760631869186-0.1369497069370.814078396262-88.951630982318.607516078423.0058745492
32.66330763049-0.3928596931490.394833497060.746480509781-0.09208195675861.261439383410.14555404568-0.1429345517210.5169863418440.06790335139150.0431713748247-0.508361427585-0.2939976075420.3292497310260.04174193458881.0770630663-0.150124921008-0.1292696367960.905428915588-0.2240427956341.09031402517-60.412892294229.773565828321.7119636874
41.58540483309-0.246750549185-1.292585285421.56394315715-0.1012424189621.908276229570.1373320942390.3332406414920.076131226767-0.2725466598350.144056529509-0.138895956611-0.1910912581770.0617559985976-0.01832236143881.1933852852-0.0591127250638-0.07556726784541.05478690881-0.06699667444461.1055627612-62.19436536131.5736010511-14.7676908937
51.9989081616-0.56817239183-0.06327972987433.31932139723-0.4261449397561.70655558579-0.03879193179990.184269849198-0.0960978054121-0.2462221878920.209595400492-0.2011282259740.009891288918670.156393003494-0.01035820604931.12769427596-0.1171342438810.01436222444321.05374512565-0.1922656932241.05222895676-57.427090237719.9842927433-11.98837763
62.42270188672-0.847307737107-0.2462109434682.987354663710.6591879568323.29015085079-0.07977789833440.009883053251290.244672873406-0.1580645010390.11453772662-0.403988743099-0.1925626738210.504003565911-0.04703530136641.01874666324-0.069146364749-0.01755224257441.0786461792-0.2483702831011.31196630233-44.85463857826.82436135342-5.27126969984
71.87532180138-0.3545129804120.7501793788764.21371011732-0.101585096052.148381829950.2665909845560.119036309657-0.04356724775920.326096693229-0.2477317966540.409116014561-0.1186953546750.28054018609-0.09546180496781.15756387504-0.1004145263820.1833912254731.03311853469-0.161471266550.961386170762-61.173202733540.5218678279-42.4603756163
81.464537260670.458839873769-0.4827493516941.93508997884-0.4529997784721.61731282186-0.0704736388964-0.06564024931970.1935826949010.1933275298920.184741271441-0.622062348703-0.07889658495230.425392870819-0.001866487285241.03782059446-0.1506212878960.01133504755730.978368405172-0.2177924175691.28651383482-45.757317050343.4066897971-31.8463856986
90.485939666636-0.8716205388390.05651581463911.882600459950.4247383948931.06074280846-0.010592011701-0.13811327776-0.4378609747560.1035873346650.0853952436-0.7599267999520.02916606804110.362926832932-0.01367896832360.941232780247-0.02829890203020.1909270011260.926666582054-0.2039914166021.28984070878-45.874246632524.0908266082-44.6181465584
101.71279219911-1.120364415830.9563134657643.337885954030.5183973280440.973696984848-0.8238178661931.032230002210.138672268844-0.392547467540.7024707127720.1971996714180.294374785719-0.6644530465090.01176127968011.211169578260.0766869983830.05709683797631.1183959545-0.1821024226931.40829161077-50.177150887612.9688456082-53.8874367444
110.135305703628-0.4424776956480.1093393926043.01929537758-0.9527723373481.07249349409-0.1389316821631.220068911140.679802243571-0.685579222941-0.260290806005-1.5090320595-0.494021394192-0.07298437061470.1226927989591.34319610853-0.08667793688630.1093185203751.170747209270.04619795907961.56016745339-45.432993954732.7401524782-55.2747542375
122.16179379667-0.3478944900410.1804318790641.359233206490.08871544383921.21741884005-0.1483143131160.3832993676540.134473337861-0.6062498303750.137628348547-0.287264767992-0.2156105137020.319003031655-0.02118575247621.33016329745-0.2722466476160.08556837972410.869524016905-0.02273606886890.718514878198-74.429244394667.0193699173-69.3572999668
132.46368849151-0.418325467513-0.1326332792291.3930332589-0.03344908147752.29069908511-0.143123666868-0.2854036691060.0828066318086-0.185074388340.124744578651-0.359354578443-0.1351812130160.173302004594-0.008252935284390.857560544534-0.165668325297-0.08555953335460.818978701386-0.1355333223570.766739729077-75.593749114165.9485599329-34.7794106498
141.859613806310.06805863443040.2080327223071.86479298578-0.8211641404752.87046020899-0.0971289444636-0.2107495440180.410959164736-0.201319112715-0.02981191725220.278094468673-0.576224432415-0.470245806795-0.05312779692711.050027829040.0050187181066-0.171157335270.746854471384-0.2278941910750.83932952661-97.033117180377.4620571905-42.352751811
153.554025405110.960677721590.8703607918860.1767584540170.07224302852991.606738407940.0607255779544-0.13089000864-0.341400032380.2077914170910.209953910040.298650845330.004017570568150.1123570368890.06833554352160.949740068526-0.0120350944563-0.08445219297611.05487360293-0.1068703272371.14074178271-123.97806334255.777581066-38.7866433625
160.875088656066-0.158585212692-0.9850787897420.6694712832940.3271061411781.941730547730.02184495773650.3390128689130.05786673239450.174682138897-0.421332954781-0.598831818949-0.2757529513670.221391383563-0.005874094442280.987722569749-0.141464978207-0.08870815893491.16780869655-0.1038419309611.05805567597-126.27407926848.6986933208-49.154472782
171.514167507660.03061256822160.166837037308-0.001835517442170.002622115365040.01140055797320.274604049843-0.721491561988-0.5559606512720.6687299315050.476518580785-0.331969975323-0.221408918545-0.163384306943-0.04217688596581.38455767036-0.061085317991-0.3140034189061.73002996408-0.2048498207671.62683253009-137.12029703360.109862413-29.8473013124
180.984318982383-0.190212050835-0.7556807468331.18011955791.172512007312.023331988680.0929107734106-0.129941142701-0.411591507513-0.226180681704-0.06506164831210.185370174453-0.2393931185550.201855947479-0.02100325551171.03794096140.0449321252934-0.1948885186840.953362939099-0.1927597864261.02730665277-113.29965005750.7341275712-56.0064690379
190.3069842263380.318119152093-0.4621662042880.29892034693-0.2149101106971.83024530235-0.394265820540.242974037110.820635918845-0.6489641579740.1775861743970.7559397061880.171522167941-2.10461273190.103720005471.448711836030.323582325069-0.5650434742681.67323283517-0.2830508310311.99095683361-128.97314491357.2162281612-66.5146336732
200.688155509489-0.10499297224-0.2209070691.63921111997-0.05980296365811.683373218590.2634535802970.2944102230040.225880274297-1.05224728852-0.2855535483650.474059021373-1.63760305825-0.8042829176540.02954350490881.905680063230.379415254229-0.4951431311131.10273077834-0.1075789133661.00046402557-117.86154854461.5147953282-74.1635056042
212.233476914980.837867233004-0.4410792740472.228525440291.75621459481.823597677780.1093044054080.140058906469-0.477418439903-0.9649432448580.034862224470.2092336801810.006077022302340.1636437094970.009299574160361.28272077486-0.0244980893885-0.2596003409260.911843002548-0.1326865573070.945329690677-108.78174376250.2746643957-73.2007235462
223.38611420419-0.495220689472-2.12659633242.838566492090.5615095927644.15050034676-0.244051214655-0.394947000149-0.449532281610.6932798454720.478644668266-0.354469464240.6369826338730.1299531330560.05088409514961.164275175130.0538754620582-0.02309112830741.022732745920.004976766420540.979726787762-147.51381655536.9797702104-35.9359586036
231.86121393814-0.109526231169-0.4891869867241.789539291960.0619139583411.39475526929-0.2852069290810.278170161821-0.143306749676-0.07010897317060.06886890809230.0640147195702-0.0407455784684-0.143592740622-0.02817288666850.8040747253460.0850639209909-0.1475499822610.709978009248-0.023984733840.792088521171-151.44656951949.1441173683-44.7594489689
241.822082642190.1769240392440.146198774871.820452018430.2719195857271.49646726372-0.2178323522830.0742788607550.805936016214-0.05743740710850.313536995526-0.603983690648-0.671662857462-0.141181538381-0.03241872527611.00747673520.114584750827-0.03380619413830.788132969674-0.07943064148940.90200851884-150.09446795359.6820811593-43.777729007
251.95901415911-0.406114005603-0.9370127990192.384375401290.678429325422.3711003971-0.0514701860440.2312033494780.00367058405444-0.189913763567-0.106159970698-0.111939411120.144283586875-0.220956483032-0.03466398294410.840477065120.0349275919739-0.08693576811710.786269611242-0.06560659805770.768319429973-149.51371625334.8152167376-58.5663506358
263.56223920835-1.868968288760.6314845178062.371123415550.5868355876040.876071516270.109806334803-0.53044816389-0.6377670090490.3914328675450.0594934275930.3981251700830.461446928502-0.189723557313-0.08294551166281.111176894770.111494614727-0.0498955927350.927879144207-0.0390724143910.854546901966-149.85154477319.6150812303-66.9041753775
272.573091351381.01474038876-0.8680041875314.02863189851-1.499189153774.87377993899-0.06518733930150.243562680852-0.2285992672530.5382379811530.694079631812-0.7255660425650.7904287348740.7713558966280.02203957744081.181693317090.174209337811-0.1803185605890.828645651690.04120576435491.07125672353-143.7466159722.8852744876-58.159014323
282.744594976911.07705744156-2.098107604471.923435773411.447784187735.088564749690.293365978949-0.2376860068330.3286415464320.564812414292-0.549893283741.11452633171-0.707572017461-1.76041900806-0.1051389503811.115452891010.08669193506610.102610522471.15116378559-0.208955697311.08154604766-160.73599977631.1102709064-51.7501789204
291.29265541103-0.06195319490960.1434523476672.11964213642-0.1374800940572.22273161896-0.1190058537680.06411661816-0.109896788507-0.2894217304140.1327006320870.998214211278-0.16653598579-0.496338644003-0.01695155467881.031445529440.150717588425-0.105228733171.008068724480.1353155866481.3777801374-173.12102608219.4855230632-8.08297414362
302.34074677222-0.1938243729740.1045517471731.88170956146-1.168406702150.936783030844-0.1279799841160.01061451885630.1901815391310.213108998210.1825532940420.789684320283-0.610312585928-0.3207984657270.04328545343691.459204541340.251184022249-0.08726487711910.7093483417510.01113447603531.0700977646-158.76992182644.9539415434-6.34885411889
313.1393434091-0.1688746316311.222414610541.31507108329-0.701970011182.346550179050.08631294505260.3388383509630.104638722247-0.0227448589438-0.0695820331421-0.318139235856-0.1830431794430.326146437464-0.1158851651771.380250743240.0393561033233-0.1320624727390.6697204619520.04658731349271.05719872113-136.97035939943.7230674637-8.57416079527
322.440230048940.0465694778122-0.6258359436681.52263390728-0.5587317084141.4759484198-0.118681873138-0.5231756655070.1654954299851.085884469280.102593751285-0.0780691608672-0.585784795509-0.111256007941-0.04666485485891.629100995090.240536439597-0.0007046481096630.809675118465-0.02031380680030.872224360399-148.60713179132.738066663317.8694956696
331.21037372603-0.4031780261181.424581774442.90731247726-1.077474252291.77479584617-0.291224609703-0.1767380930580.07717556639570.1033631831840.224080144231-0.826967765769-0.2661927787760.4758950635740.02016778444471.185752704920.0236969849449-0.1202581269190.9201657872970.009665795002611.13426345808-119.32236974513.552213360213.6906097049
342.086547950860.911554222580.2383230254941.76914815803-0.7659859485570.807886361891-0.259370411675-0.04951844090870.008996874141890.450433889580.251218885284-0.47601708251-0.357015769889-0.1377634978750.07912244754981.030559724730.02275779148-0.06660804219210.757531530575-0.1027314722790.983816196702-123.6828163543.6123402589317.9135679028
350.92008913932-0.5584095908540.4181738317031.87870263817-0.00084156631412.60587251951-0.557089383657-0.07970965794850.225911381890.1319096206460.278984468396-0.251156766944-0.8327649974910.2781077712890.1888516466281.219015842680.0671361968022-0.06856359150430.848046619045-0.02440532397630.997462903944-126.78733896212.185806567214.796980243
361.65671609435-0.005223966663920.3045637974511.79208515824-0.1781151195672.075273798190.02174174731820.2065544793680.0523733005849-0.588184258050.00960421036867-0.171807824172-0.2769192612670.309599346724-0.01691421038880.993563920768-0.06761052431070.04320751730370.6144198699940.01201396225160.743027446689-136.11379148-1.197924003964.27165348195
373.078916700550.75508364696-0.1068922063252.034361930451.483465844472.582921889560.276372054652-0.597927631949-0.909274844330.982510880365-0.135209728317-0.0358026196306-0.0396374932993-0.08330975862170.06547688178121.09415322297-0.0504804339464-0.1274771813040.8641059104640.1596093954741.03319075836-132.816657645-9.1352445469516.4046847667
380.6818524127690.227548411874-0.5836480418542.40173596212-0.292680468171.260000120550.0572243224794-0.3236501809290.06270383158281.18133383029-0.1794293561930.126138409457-0.732080499051-0.2093029778230.03984832058581.16220329525-0.03847134490080.08650263466630.7065932532520.03972499684180.706917224176-145.208943996-5.2601979353915.5674959841
391.37217482558-0.2479727132590.24853391332.73660278675-0.763782772961.487327273930.00908103712089-0.425571483457-0.3350738478250.6996954956590.3322083116141.32394653537-0.339822660751-0.489312660067-0.026211458291.085838710390.02774939328930.2453616070990.883153026529-0.001009150358231.04860311794-155.576927063-7.6481560391917.1068801044
401.24168190717-0.1881090574380.8050868197561.57107442295-0.3703552959191.6363435777-0.334089813601-0.22900884434-0.661703207129-0.01345280058490.0890876751660.8782526419820.741643576841-0.437427746526-0.04467708278690.9492124620160.040724481510.05871561864770.8095510911070.07892817122040.925268423004-155.81113688-8.458951452816.77365675553
410.6342791138920.614165032128-0.6220818064512.01307078290.9655519118711.66127030890.0590668525280.593998097633-0.515339305469-1.815512730220.16364898334-0.3967082519360.3825638066450.2702004111530.06091745405881.09707137392-0.005790077184880.1184573272111.00095890841-0.00747523198220.68269053635-138.956140503-2.58099017345-6.1866686982
424.161414694091.333992453251.302159574052.116830404430.9431142687863.55677651201-0.2867787421410.500209684177-0.2684451357920.15908636379-0.0985642269299-0.3434924020890.4557718581280.427017009858-0.01553063265521.071168590120.031165483219-0.07475583265520.758113094522-0.03795580065780.899851150171-98.6282138354-7.917287502321.7202872328
434.37220168908-0.1542244531620.4288460469911.025781096890.2791091080790.4034304787120.0652430156477-0.890807652053-1.385275655690.659914218392-0.13243229639-0.3303451921370.7495457671060.5178806416380.02559854378381.431299775790.0849867697830.02615769009780.8604636317520.09210502108140.74152149295-106.334353257-14.327616070436.1475266709
441.94401934897-0.3930105361750.413040433962.384246296-0.07024141633231.80637260893-0.185920233756-0.4727333360970.1254841255050.414971566675-0.2195680124140.357287094623-0.161674714032-0.119388083565-0.01952730746031.1012528741-0.0243048373840.06386764991660.848873633459-0.1216450242540.615240414435-113.409440995-5.3964418485234.8464280651
451.33524650047-0.2464346877480.05301106202942.107618623910.8663803889991.18691812051-0.142809479354-0.0528041538857-0.176132402659-0.0768651080083-0.2924590426490.5344443944030.481282548588-0.259887279905-0.02125184090691.07871071102-0.08061374398220.1344559003430.667045198483-0.01026843688610.810348175254-113.010728856-25.067466575720.7670959093
462.314069166630.9139890705230.2875597793471.581013612641.417240942062.071171478480.1395348522550.109343530002-0.6954448962520.258033765749-0.00477991522024-0.05647236664480.8479467977990.2865802925010.006469419032111.24476595996-0.03485091642940.186963104640.853669563997-0.08450588975391.00638518887-110.170020956-35.01039222179.97368220327
474.381947622681.056589190262.840655682233.515441810011.090797257441.984993016130.105141809277-1.47698921854-0.9099411743371.54057799064-0.677534645677-1.706325800170.9826794730230.718046229715-0.02107990623091.533272085960.06343861313860.01450248554971.093909260450.152561350481.04887469555-101.076501663-28.672460258626.6453814868
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 716 )AA1 - 7161 - 402
22chain 'A' and (resid 717 through 856 )AA717 - 856403 - 542
33chain 'A' and (resid 857 through 1140 )AA857 - 1140543 - 826
44chain 'B' and (resid 715 through 794 )BC715 - 7941 - 80
55chain 'B' and (resid 795 through 890 )BC795 - 89081 - 176
66chain 'B' and (resid 891 through 1039 )BC891 - 1039177 - 325
77chain 'C' and (resid 20 through 42 )CE20 - 421 - 23
88chain 'C' and (resid 43 through 150 )CE43 - 15024 - 131
99chain 'C' and (resid 151 through 218 )CE151 - 218132 - 199
1010chain 'C' and (resid 219 through 243 )CE219 - 243200 - 224
1111chain 'C' and (resid 244 through 267 )CE244 - 267225 - 248
1212chain 'D' and (resid 1 through 365 )DG1 - 3651 - 365
1313chain 'D' and (resid 366 through 819 )DG366 - 819366 - 506
1414chain 'D' and (resid 820 through 1140 )DG820 - 1140507 - 827
1515chain 'E' and (resid 715 through 768 )EI715 - 7681 - 54
1616chain 'E' and (resid 769 through 794 )EI769 - 79455 - 80
1717chain 'E' and (resid 795 through 808 )EI795 - 80881 - 94
1818chain 'E' and (resid 809 through 880 )EI809 - 88095 - 166
1919chain 'E' and (resid 881 through 901 )EI881 - 901167 - 187
2020chain 'E' and (resid 902 through 972 )EI902 - 972188 - 258
2121chain 'E' and (resid 973 through 1033 )EI973 - 1033259 - 319
2222chain 'F' and (resid 20 through 42 )FK20 - 421 - 23
2323chain 'F' and (resid 43 through 106 )FK43 - 10624 - 87
2424chain 'F' and (resid 107 through 151 )FK107 - 15188 - 132
2525chain 'F' and (resid 152 through 218 )FK152 - 218133 - 199
2626chain 'F' and (resid 219 through 233 )FK219 - 233200 - 214
2727chain 'F' and (resid 234 through 243 )FK234 - 243215 - 224
2828chain 'F' and (resid 244 through 267 )FK244 - 267225 - 248
2929chain 'G' and (resid 1 through 307 )GN1 - 3071 - 307
3030chain 'G' and (resid 308 through 761 )GN308 - 761308 - 447
3131chain 'G' and (resid 762 through 856 )GN762 - 856448 - 542
3232chain 'G' and (resid 857 through 1140 )GN857 - 1140543 - 826
3333chain 'H' and (resid 715 through 751 )HP715 - 7511 - 37
3434chain 'H' and (resid 752 through 794 )HP752 - 79438 - 80
3535chain 'H' and (resid 795 through 832 )HP795 - 83281 - 118
3636chain 'H' and (resid 833 through 872 )HP833 - 872119 - 158
3737chain 'H' and (resid 873 through 890 )HP873 - 890159 - 176
3838chain 'H' and (resid 891 through 931 )HP891 - 931177 - 217
3939chain 'H' and (resid 932 through 970 )HP932 - 970218 - 256
4040chain 'H' and (resid 971 through 1010 )HP971 - 1010257 - 296
4141chain 'H' and (resid 1011 through 1034 )HP1011 - 1034297 - 320
4242chain 'I' and (resid 20 through 42 )IS20 - 421 - 23
4343chain 'I' and (resid 43 through 63 )IS43 - 6324 - 44
4444chain 'I' and (resid 64 through 150 )IS64 - 15045 - 131
4545chain 'I' and (resid 151 through 217 )IS151 - 217132 - 198
4646chain 'I' and (resid 218 through 243 )IS218 - 243199 - 224
4747chain 'I' and (resid 244 through 267 )IS244 - 267225 - 248

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Feb 9, 2022. New format data for meta-information of EMDB entries

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