PDB-3blq: Crystal Structure of Human CDK9/cyclinT1 in Complex with ATP

ID or keywords:

Entry

Database: PDB / ID: 3blq

Title

Crystal Structure of Human CDK9/cyclinT1 in Complex with ATP

Components

Cell division protein kinase 9
Cyclin-T1

Keywords

TRANSCRIPTION / transcriptional CDK-cyclin complex / phosphorylated / in complex with ATP / Alternative splicing / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transcription regulation / Transferase / Acetylation / Cell cycle / Cell division / Coiled coil / Host-virus interaction

Function / homology

Function and homology information

P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription ...P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / transcription elongation-coupled chromatin remodeling / regulation of cyclin-dependent protein serine/threonine kinase activity / replication fork processing / cellular response to cytokine stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 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 / regulation of DNA repair / 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 / cyclin binding / transcription elongation factor complex / molecular condensate scaffold activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Baumli, S. / Lolli, G. / Lowe, E.D. / Johnson, L.N.

Citation

Journal: Embo J. / Year: 2008
Title: The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation
Authors: Baumli, S. / Lolli, G. / Lowe, E.D. / Troiani, S. / Rusconi, L. / Bullock, A.N. / Debreczeni, J.E. / Knapp, S. / Johnson, L.N.

History

Deposition	Dec 11, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Nov 10, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3blq.cif.gz	245.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3blq_validation.pdf.gz	781.1 KB	Display	wwPDB validaton report
Full document	3blq_full_validation.pdf.gz	789.8 KB	Display
Data in XML	3blq_validation.xml.gz	22.4 KB	Display
Data in CIF	3blq_validation.cif.gz	30 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/3blq ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blq	HTTPS FTP

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Related structure data

Related structure data	2ivxC 3blhSC 3blrC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4bci-d 3blr-d 3tni-d 5efq-2 3blh-d 4bcj-d 3my1-d 4bch-d 6b3e-2 4imy-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (6) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (5) #47 - Nov 2003 Simian Virus 40 similarity (3) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (2) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#236 - Aug 2019
Cyclin and Cyclin-dependent Kinase
similarity (6)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (11)
#67 - Jul 2005
TATA-Binding Protein
similarity (5)
#47 - Nov 2003
Simian Virus 40
similarity (3)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (2)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (2)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)

Deposited unit

A: Cell division protein kinase 9

B: Cyclin-T1

hetero molecules

68.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	173.130, 173.130, 95.640
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

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Protein , 2 types, 2 molecules AB

#1: Protein	Cell division protein kinase 9 / Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / C-2K / Cell division cycle 2- ...Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / C-2K / Cell division cycle 2-like protein kinase 4 Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein	Cyclin-T1 / CycT1 / Cyclin-T Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-259 / Mutation: Q77R, E96G, F241L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60563

#1: Protein

Cell division protein kinase 9 / Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / C-2K / Cell division cycle 2- ...

Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CDK9 / Plasmid: pVL1392 / Production host:

Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase

#2: Protein

Cyclin-T1 / CycT1 / Cyclin-T

Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-259 / Mutation: Q77R, E96G, F241L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CCNT1 / Plasmid: pVL1392 / Production host:

Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60563

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Non-polymers , 4 types, 33 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.05 Å³/Da / Density % sol: 69.6 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, 20% PEG 1000, 0.5M NaCl, 4mM TCEP, 2mM AMPPNP, 2.4mM MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.9→32.7 Å / Num. obs: 23641 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / R_merge(I) obs: 0.085 / Net I/σ(I): 16.7
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.512 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.004	data extraction
ProDC		data collection
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BLH

3blh

Resolution: 2.9→29.501 Å / FOM work R set: 0.845 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.234	2366	5.04 %	RANDOM
R_work	0.174	-	-	-
obs	-	23638	99.21 %	-

Solvent computation

B_sol: 47.843 Å² / k_sol: 0.314 e/Å³

Displacement parameters

B_iso max: 456.6 Å² / B_iso mean: 84.32 Å² / B_iso min: 25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.056 Å²	0 Å²	0 Å²
2-	-	-1.056 Å²	-0 Å²
3-	-	-	2.113 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.501 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4455	0	40	30	4525

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.745	1
X-RAY DIFFRACTION	f_bond_d	0.006	1
X-RAY DIFFRACTION	f_chiral_restr	0.055	1
X-RAY DIFFRACTION	f_dihedral_angle_d	11.205	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.068	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.9-2.911	0.252	517	X-RAY DIFFRACTION	89	95
2.911-2.922	0.266	470	X-RAY DIFFRACTION	89	95
2.922-2.934	0.268	511	X-RAY DIFFRACTION	89	96
2.934-2.945	0.262	511	X-RAY DIFFRACTION	89	93
2.945-2.957	0.258	487	X-RAY DIFFRACTION	89	92
2.957-2.968	0.249	513	X-RAY DIFFRACTION	89	94
2.968-2.98	0.279	495	X-RAY DIFFRACTION	89	94
2.98-2.993	0.246	531	X-RAY DIFFRACTION	89	94
2.993-3.005	0.263	447	X-RAY DIFFRACTION	89	94
3.005-3.018	0.235	490	X-RAY DIFFRACTION	89	97
3.018-3.03	0.23	545	X-RAY DIFFRACTION	89	93
3.03-3.043	0.248	488	X-RAY DIFFRACTION	89	95
3.043-3.057	0.233	522	X-RAY DIFFRACTION	89	94
3.057-3.07	0.253	470	X-RAY DIFFRACTION	89	94
3.07-3.084	0.22	532	X-RAY DIFFRACTION	89	92
3.084-3.098	0.21	490	X-RAY DIFFRACTION	89	95
3.098-3.112	0.235	480	X-RAY DIFFRACTION	89	96
3.112-3.127	0.218	495	X-RAY DIFFRACTION	89	94
3.127-3.142	0.238	511	X-RAY DIFFRACTION	89	93
3.142-3.157	0.192	529	X-RAY DIFFRACTION	89	94
3.157-3.172	0.206	494	X-RAY DIFFRACTION	89	95
3.172-3.188	0.224	509	X-RAY DIFFRACTION	89	93
3.188-3.204	0.227	503	X-RAY DIFFRACTION	89	94
3.204-3.22	0.199	475	X-RAY DIFFRACTION	89	95
3.22-3.237	0.207	502	X-RAY DIFFRACTION	89	95
3.237-3.254	0.216	502	X-RAY DIFFRACTION	89	95
3.254-3.271	0.194	526	X-RAY DIFFRACTION	89	96
3.271-3.289	0.196	547	X-RAY DIFFRACTION	89	95
3.289-3.307	0.219	475	X-RAY DIFFRACTION	89	94
3.307-3.326	0.218	468	X-RAY DIFFRACTION	89	96
3.326-3.345	0.193	501	X-RAY DIFFRACTION	89	95
3.345-3.364	0.197	530	X-RAY DIFFRACTION	89	94
3.364-3.384	0.208	504	X-RAY DIFFRACTION	89	93
3.384-3.404	0.195	478	X-RAY DIFFRACTION	89	94
3.404-3.425	0.179	483	X-RAY DIFFRACTION	89	96
3.425-3.446	0.18	532	X-RAY DIFFRACTION	89	94
3.446-3.468	0.186	512	X-RAY DIFFRACTION	89	97
3.468-3.491	0.177	546	X-RAY DIFFRACTION	89	94
3.491-3.514	0.173	441	X-RAY DIFFRACTION	89	91
3.514-3.538	0.18	493	X-RAY DIFFRACTION	89	91
3.538-3.562	0.176	428	X-RAY DIFFRACTION	89	91
3.562-3.587	0.171	584	X-RAY DIFFRACTION	89	95
3.587-3.613	0.163	520	X-RAY DIFFRACTION	89	96
3.613-3.639	0.158	476	X-RAY DIFFRACTION	89	95
3.639-3.667	0.148	486	X-RAY DIFFRACTION	89	95
3.667-3.695	0.179	507	X-RAY DIFFRACTION	89	93
3.695-3.724	0.153	498	X-RAY DIFFRACTION	89	92
3.724-3.754	0.167	556	X-RAY DIFFRACTION	89	97
3.754-3.785	0.158	461	X-RAY DIFFRACTION	89	95
3.785-3.817	0.159	521	X-RAY DIFFRACTION	89	95
3.817-3.85	0.153	513	X-RAY DIFFRACTION	89	95
3.85-3.884	0.156	503	X-RAY DIFFRACTION	89	92
3.884-3.92	0.153	462	X-RAY DIFFRACTION	89	95
3.92-3.957	0.149	523	X-RAY DIFFRACTION	89	96
3.957-3.995	0.155	483	X-RAY DIFFRACTION	89	93
3.995-4.035	0.129	563	X-RAY DIFFRACTION	89	94
4.035-4.076	0.132	442	X-RAY DIFFRACTION	89	95
4.076-4.12	0.16	497	X-RAY DIFFRACTION	89	93
4.12-4.165	0.13	531	X-RAY DIFFRACTION	89	96
4.165-4.212	0.125	495	X-RAY DIFFRACTION	89	95
4.212-4.261	0.142	489	X-RAY DIFFRACTION	89	96
4.261-4.313	0.134	497	X-RAY DIFFRACTION	89	93
4.313-4.367	0.127	555	X-RAY DIFFRACTION	89	96
4.367-4.425	0.143	455	X-RAY DIFFRACTION	89	94
4.425-4.485	0.129	518	X-RAY DIFFRACTION	89	96
4.485-4.549	0.124	539	X-RAY DIFFRACTION	89	95
4.549-4.617	0.137	474	X-RAY DIFFRACTION	89	95
4.617-4.689	0.123	505	X-RAY DIFFRACTION	89	93
4.689-4.765	0.139	529	X-RAY DIFFRACTION	89	93
4.765-4.847	0.119	444	X-RAY DIFFRACTION	89	95
4.847-4.935	0.136	549	X-RAY DIFFRACTION	89	94
4.935-5.029	0.128	481	X-RAY DIFFRACTION	89	95
5.029-5.131	0.14	475	X-RAY DIFFRACTION	89	92
5.131-5.242	0.141	564	X-RAY DIFFRACTION	89	96
5.242-5.364	0.17	462	X-RAY DIFFRACTION	89	95
5.364-5.497	0.14	500	X-RAY DIFFRACTION	89	95
5.497-5.644	0.17	536	X-RAY DIFFRACTION	89	96
5.644-5.809	0.163	500	X-RAY DIFFRACTION	89	94
5.809-5.995	0.16	499	X-RAY DIFFRACTION	89	94
5.995-6.208	0.175	508	X-RAY DIFFRACTION	89	95
6.208-6.454	0.177	486	X-RAY DIFFRACTION	89	95
6.454-6.744	0.18	473	X-RAY DIFFRACTION	89	91
6.744-7.095	0.17	510	X-RAY DIFFRACTION	89	95
7.095-7.532	0.158	531	X-RAY DIFFRACTION	89	95
7.532-8.103	0.148	490	X-RAY DIFFRACTION	89	93
8.103-8.898	0.128	490	X-RAY DIFFRACTION	89	95
8.898-10.139	0.123	499	X-RAY DIFFRACTION	89	93
10.139-12.607	0.134	493	X-RAY DIFFRACTION	89	93
12.607-29.502	0.229	439	X-RAY DIFFRACTION	89	82

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.4354	-0.0773	0.2117	1.2988	0.4837	2.6247	0.2677	0.0668	-0.6278	0.2104	-0.1728	-0.1872	0.7499	0.1817	-0.0962	0.3306	-0.0056	-0.0935	0.213	0.0706	0.4583	46.8817	-17.5246	-1.5063
2	2.1487	-0.4348	-0.118	1.1302	0.2001	1.2323	0.0383	0.244	0.2651	0.0105	0.0855	-0.2873	-0.0902	0.1227	-0.1151	0.2072	-0.0113	-0.027	0.3008	-0.0513	0.2741	21.4156	3.4648	-20.4795

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A	A	7 - 326
2	X-RAY DIFFRACTION	2	chain B	B	9 - 259

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Protein , 2 types, 2 molecules AB

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Non-polymers , 4 types, 33 molecules

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