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- PDB-1ua2: Crystal Structure of Human CDK7 -

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Basic information

Entry
Database: PDB / ID: 1ua2
TitleCrystal Structure of Human CDK7
ComponentsCell division protein kinase 7
KeywordsCELL CYCLE / TRANSFERASE / PHOSPHORYLATION / PROTEIN-PROTEIN INTERACTION / PROTEIN KINASE
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 / cytoplasm / cytosol
Similarity search - Function
Cyclin-dependent kinase 7 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Cyclin-dependent kinase 7 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyclin-dependent kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsLolli, G. / Lowe, E.D. / Brown, N.R. / Johnson, L.N.
CitationJournal: Structure / Year: 2004
Title: The Crystal Structure of Human CDK7 and Its Protein Recognition Properties
Authors: Lolli, G. / Lowe, E.D. / Brown, N.R. / Johnson, L.N.
History
DepositionAug 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 7
B: Cell division protein kinase 7
C: Cell division protein kinase 7
D: Cell division protein kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,7108
Polymers156,6814
Non-polymers2,0294
Water86548
1
A: Cell division protein kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6782
Polymers39,1701
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6782
Polymers39,1701
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division protein kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6782
Polymers39,1701
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell division protein kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6782
Polymers39,1701
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.501, 191.635, 75.794
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 6 / Auth seq-ID: 13 - 311 / Label seq-ID: 13 - 311

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe biological unit is a monomer . The presence of four copies in the assymetric unit has no biological signifigance

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Components

#1: Protein
Cell division protein kinase 7 / E.C.2.7.1.37 / CDK-activating kinase / CAK / TFIIH basal transcription factor complex kinase subunit / 39 kDa ...CDK-activating kinase / CAK / TFIIH basal transcription factor complex kinase subunit / 39 kDa protein kinase / P39 Mo15 / STK1 / CAK1 / serine/threonine kinase stk1 / serine/threonine protein kinase 1


Mass: 39170.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Sf21 cells in culture / Gene: CDK7 / Plasmid: pVL1392 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50613, EC: 2.7.1.37
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9756
SYNCHROTRONESRF ID1320.9789
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDNov 22, 2003
MARRESEARCH2CCDDec 6, 2003Microfocus beamline ID13 at ESRF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97561
20.97891
ReflectionResolution: 2.96→49.45 Å / Num. all: 38122 / Num. obs: 35416 / % possible obs: 92.9 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 73.1 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 9.5
Reflection shellResolution: 3.02→3.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3851 / Rsym value: 0.466 / % possible all: 70.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human CDK2

Resolution: 3.02→49.45 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.844 / SU B: 42.022 / SU ML: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 1757 5 %RANDOM
Rwork0.21274 ---
all0.21659 33271 --
obs0.21659 33271 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.013 Å2
Baniso -1Baniso -2Baniso -3
1-4.22 Å20 Å2-0.05 Å2
2---2.56 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 3.02→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9164 0 124 48 9336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229524
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.97712964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.77351140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6224420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.144151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7481552
X-RAY DIFFRACTIONr_chiral_restr0.1360.21444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027112
X-RAY DIFFRACTIONr_nbd_refined0.2840.25515
X-RAY DIFFRACTIONr_nbtor_refined0.3350.26416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2413
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.2145
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.27
X-RAY DIFFRACTIONr_mcbond_it0.6981.55847
X-RAY DIFFRACTIONr_mcangle_it1.27729260
X-RAY DIFFRACTIONr_scbond_it1.46334130
X-RAY DIFFRACTIONr_scangle_it2.4534.53704
Refine LS restraints NCS

Ens-ID: 1 / Number: 2291 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.695
2Bloose positional0.725
3Cloose positional0.715
4Dloose positional0.715
1Aloose thermal5.3710
2Bloose thermal2.510
3Cloose thermal3.9510
4Dloose thermal5.1410
LS refinement shellResolution: 3.02→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 78 -
Rwork0.312 1744 -
obs--83.2 %
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)
10.8479-0.4832-0.28161.2664-0.06240.80220.02070.0805-0.02170.0543-0.0597-0.1532-0.0642-0.04130.0391-0.0841-0.0081-0.0077-0.01630.001-0.002129.43150.517921.9775
20.9058-0.69420.21111.1296-0.59451.63610.15420.0679-0.1615-0.2119-0.07060.14770.0837-0.0323-0.0835-0.0050.0251-0.0197-0.0283-0.0415-0.005151.921279.135132.6391
30.5010.34480.20741.2238-0.02521.7291-0.0990.00820.0576-0.03260.08860.148-0.2519-0.16030.0104-0.0163-0.00340.01260.01080.0036-0.018133.2214128.74910.5457
40.9621-0.9733-0.51281.96460.18762.44760.18520.09580.1207-0.2707-0.0564-0.0369-0.00910.0224-0.1288-0.03010.04250.0172-0.02610.02280.019310.888847.318537.4155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 31113 - 311
2X-RAY DIFFRACTION2BB13 - 31113 - 311
3X-RAY DIFFRACTION3CC13 - 31113 - 311
4X-RAY DIFFRACTION4DD13 - 31113 - 311

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