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- PDB-8r9b: A soakable crystal form of human CDK7 in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 8r9b
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 / Tat-mediated elongation of the HIV-1 transcript / cyclin-dependent kinase / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin-dependent protein serine/threonine kinase activity / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A:Cdk2-associated events at S phase entry / 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 / 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 / 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 / regulation of cell cycle / protein kinase activity / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cyclin-dependent kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.21 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
C: Cyclin-dependent kinase 7
D: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,63014
Polymers160,2564
Non-polymers2,37410
Water6,485360
1
A: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5943
Polymers40,0641
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6874
Polymers40,0641
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6623
Polymers40,0641
Non-polymers5982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6874
Polymers40,0641
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.140, 180.285, 76.335
Angle α, β, γ (deg.)90.00, 117.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cyclin-dependent kinase 7


Mass: 40063.988 Da / Num. of mol.: 4 / Mutation: S164D, T170E, del327-346
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.21→90.14 Å / Num. obs: 64931 / % possible obs: 86.1 % / Redundancy: 3.5 % / Rrim(I) all: 0.091 / Net I/σ(I): 10.5
Reflection shellResolution: 2.26→2.391 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3316 / Rrim(I) all: 1.048 / % possible all: 47

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.21→90.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.258 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24265 3529 5.2 %RANDOM
Rwork0.19236 ---
obs0.19491 64931 75.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.52 Å2
2--0.09 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.21→90.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9208 0 145 360 9713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0159588
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178818
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.7813019
X-RAY DIFFRACTIONr_angle_other_deg0.5111.73220630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.0395.4581179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05521.303422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81515.0711558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7591555
X-RAY DIFFRACTIONr_chiral_restr0.070.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02110457
X-RAY DIFFRACTIONr_gen_planes_other00.021771
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_it3.6626.5514602
X-RAY DIFFRACTIONr_mcbond_other3.6626.5514603
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.817.6284986
X-RAY DIFFRACTIONr_scbond_other4.817.6284987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.84234.9710256
X-RAY DIFFRACTIONr_long_range_B_other7.84234.94110243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.211→2.269 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 34 -
Rwork0.348 647 -
obs--10.17 %
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)
12.55390.30560.31283.10760.03991.2270.04960.2943-0.3263-0.3030.04350.00970.12730.0859-0.09310.0536-0.0166-0.03150.11360.00440.07116.9734-6.497629.3558
22.23940.6864-0.36233.3373-0.24771.25720.07920.30180.2583-0.4221-0.01850.0485-0.1186-0.11-0.06070.1044-0.00480.04870.1076-0.01410.0746-15.923831.149133.2371
33.52110.5927-0.37723.4995-0.83571.2487-0.07050.06540.0801-0.00050.098-0.20080.04930.0701-0.02750.10460.0291-0.00330.12110.00720.0226-32.9836-17.606350.6949
43.92810.50040.35072.90390.71421.46-0.06130.09250.0633-0.16130.01370.3118-0.105-0.12690.04770.1290.01320.03950.0941-0.00340.0625-38.990742.778156.6065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 311
2X-RAY DIFFRACTION2B3 - 310
3X-RAY DIFFRACTION3C8 - 311
4X-RAY DIFFRACTION4D9 - 311

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