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- PDB-8r9u: A soakable crystal form of human CDK7 in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 8r9u
TitleA soakable crystal form of human CDK7 in complex with AMP-PNP
ComponentsCyclin-dependent kinase 7
KeywordsCELL CYCLE / serine-threonine kinase / phosphorylation / cell cycle progression / ATP binding
Function / homology
Function and homology information


snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / 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 / transcription factor TFIIH core complex / transcription factor TFIIH holo complex ...snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / 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 / transcription factor TFIIH core complex / transcription factor TFIIH holo 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 G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / Tat-mediated elongation of the HIV-1 transcript / cyclin-dependent protein serine/threonine kinase activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Transcription Elongation / cyclin-dependent protein kinase holoenzyme complex / Formation of RNA Pol II elongation complex / 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 / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / fibrillar center / 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 kinase activity / regulation of cell cycle / protein stabilization / cell division / 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
: / Cyclin-dependent kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.937 Å
AuthorsMukherjee, M. / Cleasby, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design.
Authors: Mukherjee, M. / Day, P.J. / Laverty, D. / Bueren-Calabuig, J.A. / Woodhead, A.J. / Griffiths-Jones, C. / Hiscock, S. / East, C. / Boyd, S. / O'Reilly, M.
History
DepositionNov 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)85,4524
Polymers84,4712
Non-polymers9812
Water5,296294
1
A: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7262
Polymers42,2361
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7262
Polymers42,2361
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.303, 127.711, 142.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclin-dependent kinase 7


Mass: 42235.637 Da / Num. of mol.: 2 / Mutation: W132R,S164D, T170E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK7 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): 6 / References: UniProt: P50613
#2: Chemical ChemComp-YNK / 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile


Mass: 490.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26F3N6OP / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M (NH4)3 citrate 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.93→71.34 Å / Num. obs: 28311 / % possible obs: 83.8 % / Redundancy: 5 % / Rrim(I) all: 0.202 / Net I/σ(I): 7.28
Reflection shellResolution: 1.94→2.21 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1413 / Rrim(I) all: 0.946

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (16-JUL-2021)refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.937→71.34 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.802 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.558 / SU Rfree Blow DPI: 0.349
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.3401 1386 4.9 %RANDOM
Rwork0.275 ---
obs0.2782 28311 50.6 %-
Displacement parametersBiso mean: 40.416 Å2
Baniso -1Baniso -2Baniso -3
1--3.5751 Å20 Å20 Å2
2---2.1928 Å20 Å2
3---5.7679 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 1.937→71.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 68 294 4852
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0139578HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1717431HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2106SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1497HARMONIC16
X-RAY DIFFRACTIONt_it9578HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion7.09
X-RAY DIFFRACTIONt_other_torsion18.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion616SEMIHARMONIC5
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_contact7438SEMIHARMONIC4
LS refinement shellResolution: 1.94→2.13 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3358 -3.88 %
Rwork0.3259 545 -
all0.3263 567 -
obs--4.1 %
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)
11.52130.9228-0.73042.15650.16294.2412-0.18990.21870.1572-0.16030.04680.0131-0.4927-0.33020.1431-0.02630.1045-0.0835-0.14960.09530.115314.521113.2441-34.7171
20.67020.11360.11540.34380.92781.8895-0.0907-0.00570.07710.03460.04920.0210.2427-0.01290.0415-0.0999-0.0098-0.021-0.07110.0390.098721.1339-11.7712-31.5473
30.7116-0.569-0.73473.8770.77750-0.0549-0.18930.063-0.04830.14380.0822-0.32150.5369-0.0889-0.1742-0.06590.03820.0634-0.1520.089126.01614.1924-66.3998
40.6143-0.3699-0.02150.5052-0.92121.78080.0644-0.1351-0.0248-0.1722-0.06340.11650.16710.052-0.001-0.1514-0.03750.0063-0.01030.01440.100118.9834-10.6993-70.8902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|10 - A|95 }
2X-RAY DIFFRACTION2{ A|96 - A|311 }
3X-RAY DIFFRACTION3{ B|10 - B|95 }
4X-RAY DIFFRACTION4{ B|96 - B|311 }

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