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- PDB-8r9s: A soakable crystal form of human CDK7 in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 8r9s
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


RNA polymerase II CTD heptapeptide repeat S5 kinase activity / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / 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 ...RNA polymerase II CTD heptapeptide repeat S5 kinase activity / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / 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 / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / 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 / cyclin-dependent protein kinase holoenzyme complex / RNA Polymerase II Transcription Elongation / 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / 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
Chem-PE3 / DI(HYDROXYETHYL)ETHER / : / Cyclin-dependent kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.78 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
Revision 1.3Oct 23, 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

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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)88,1169
Polymers84,4712
Non-polymers3,6447
Water1,26170
1
A: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1115
Polymers42,2361
Non-polymers1,8754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0054
Polymers42,2361
Non-polymers1,7693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.294, 145.584, 66.833
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

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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): 9 / References: UniProt: P50613
#2: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H58O15
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-YPK / [(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate / HYDROXYETHYLAMINE BACE INHIBITOR


Mass: 499.649 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H41N7O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% Glycerol .02M KNa tartrate .02M NH4 acetate .02M Na formate .02M Na oxamate .02M Na3 citrate 10% PEG 4000 .1M pH=7.5 MOPS/NaHEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.78→35.95 Å / Num. obs: 12346 / % possible obs: 84.7 % / Redundancy: 3.2 % / Rrim(I) all: 0.3 / Net I/σ(I): 3.54
Reflection shellResolution: 2.78→3.028 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 618 / Rrim(I) all: 0.632

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.78→35.12 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.758 / SU B: 53.867 / SU ML: 0.538 / Cross valid method: THROUGHOUT / ESU R Free: 0.625 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 592 4.8 %RANDOM
Rwork0.23721 ---
obs0.24008 11716 63.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-0.12 Å2
2--1.33 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.78→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 143 70 4834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0154873
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174566
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.7656573
X-RAY DIFFRACTIONr_angle_other_deg0.5031.73110693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7615.052575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60520.393224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.21315.05799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6851531
X-RAY DIFFRACTIONr_chiral_restr0.0670.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215268
X-RAY DIFFRACTIONr_gen_planes_other00.02872
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it00.1172310
X-RAY DIFFRACTIONr_mcbond_other00.1172311
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2230.172563
X-RAY DIFFRACTIONr_scbond_other0.2230.172564
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined0.2440.6435451
X-RAY DIFFRACTIONr_long_range_B_other0.2440.6435449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9098 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 4 -
Rwork0.346 132 -
obs--9.48 %
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)
11.42160.5215-0.20682.1916-0.88383.7108-0.03410.35520.3359-0.4909-0.09990.066-0.22920.22830.13390.17080.0273-0.01740.18420.01050.248516.211933.7037-13.8889
21.55720.2715-0.25852.01960.51090.92620.0361-0.1727-0.03950.1112-0.0599-0.0563-0.00630.03520.02380.0081-0.00590.00360.02020.01170.14968.531628.139410.856
32.37140.8428-0.36043.78471.71172.72010.05020.4824-0.2625-0.4620.00090.03270.2043-0.154-0.05120.1970.0496-0.05960.19790.0130.18293.730562.6812-13.6817
41.57320.3302-0.13542.0988-0.60671.26040.046-0.16720.02370.1762-0.05120.0486-0.1304-0.05430.00520.0219-0.0010.01630.0228-0.00520.16311.62868.418210.7925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 95
2X-RAY DIFFRACTION2A96 - 312
3X-RAY DIFFRACTION3B9 - 95
4X-RAY DIFFRACTION4B96 - 312

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