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- PDB-8p4z: Crystal structure of the human CDK7 kinase domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 8p4z
TitleCrystal structure of the human CDK7 kinase domain in complex with LDC4297
ComponentsCyclin-dependent kinase 7
KeywordsCELL CYCLE / transferase / cyclin-dependent kinase / cell division
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE ...cyclin-dependent protein kinase activating kinase holoenzyme complex / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / ATP-dependent activity, acting on DNA / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription by RNA polymerase II / protein stabilization / regulation of cell cycle / protein kinase activity / cell cycle / cell division / phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cyclin-dependent kinase 7 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
TRIETHYLENE GLYCOL / Chem-WZ8 / Cyclin-dependent kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLaursen, M. / Caing-Carlsson, R. / Houssari, R. / Javadi, A. / Kimbung, Y.R. / Murina, V. / Orozco-Rodriguez, J.M. / Svensson, A. / Welin, M. / Logan, D. ...Laursen, M. / Caing-Carlsson, R. / Houssari, R. / Javadi, A. / Kimbung, Y.R. / Murina, V. / Orozco-Rodriguez, J.M. / Svensson, A. / Welin, M. / Logan, D. / Svensson, B. / Walse, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the human CDK7 kinase domain in complex with LDC4297
Authors: Laursen, M. / Caing-Carlsson, R. / Houssari, R. / Javadi, A. / Kimbung, Y.R. / Murina, V. / Orozco-Rodriguez, J.M. / Svensson, A. / Welin, M. / Logan, D. / Svensson, B. / Walse, B.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.entity_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 7
B: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73814
Polymers68,7472
Non-polymers1,99012
Water48627
1
A: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1415
Polymers34,3741
Non-polymers7674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5979
Polymers34,3741
Non-polymers1,2238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.170, 188.170, 188.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclin-dependent kinase 7 / / 39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / ...39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / Serine/threonine-protein kinase 1 / TFIIH basal transcription factor complex kinase subunit


Mass: 34373.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK7, CAK, CAK1, CDKN7, MO15, STK1 / Cell line (production host): ExpiSf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase

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Non-polymers , 5 types, 39 molecules

#2: Chemical ChemComp-WZ8 / 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine


Mass: 432.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate, 12% w/v PEG 3350, 0.2 M NDSB-201

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2022
RadiationMonochromator: Si (111), hDCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.75→19.95 Å / Num. obs: 30114 / % possible obs: 99.7 % / Redundancy: 40 % / Biso Wilson estimate: 75.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.027 / Rrim(I) all: 0.169 / Χ2: 1.09 / Net I/σ(I): 21.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 41 % / Rmerge(I) obs: 4.909 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4330 / CC1/2: 0.571 / Rpim(I) all: 0.773 / Rrim(I) all: 4.97 / Χ2: 0.92 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (22-FEB-2023)refinement
Aimless0.7.9 (10-JUN-2022)data scaling
XDS10-JAN-2022data reduction
PHASER2.8.3 (20-AUG-2021)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→19.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.381 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1479 4.92 %RANDOM
Rwork0.2247 ---
obs0.226 30063 100 %-
Displacement parametersBiso mean: 105.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 138 27 4558
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074659HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.836297HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1625SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes777HARMONIC5
X-RAY DIFFRACTIONt_it4659HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion18.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion581SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3197SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.77 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4726 -5.48 %
Rwork0.374 569 -
all0.3792 602 -
obs--98.86 %
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)
11.79630.49040.31972.9834-0.09169.23190.13420.0718-0.1415-0.0423-0.3354-0.6219-0.46560.70570.20120.0086-0.0486-0.1831-0.04340.1325-0.0347-19.1002-0.2834.4299
24.0230.2473-1.06561.4749-0.43472.10330.32020.04020.0733-0.2485-0.1755-0.0357-0.0742-0.0007-0.1447-0.07850.0008-0.0462-0.13410.0438-0.1417-2.808211.337367.8368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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