[English] 日本語
Yorodumi
- PDB-3blr: Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3blr
TitleCrystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol
Components
  • Cell division protein kinase 9
  • Cyclin-T1
KeywordsTRANSCRIPTION / transcriptional CDK-cyclin complex / phosphorylated / Flavopiridol / 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 / RNA polymerase binding / negative regulation of protein localization to chromatin / [RNA-polymerase]-subunit kinase / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / replication fork processing / cellular response to cytokine stimulus / regulation of cyclin-dependent protein serine/threonine kinase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / regulation of DNA repair / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / molecular condensate scaffold activity / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription elongation factor complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / PML body / kinase activity / DNA-binding transcription factor binding / cell population proliferation / Estrogen-dependent gene expression / 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
: / Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...: / Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-CPB / PHOSPHATE ION / Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBaumli, S. / Lolli, G. / Lowe, E.D. / Johnson, L.N.
CitationJournal: 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
DepositionDec 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein kinase 9
B: Cyclin-T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8606
Polymers68,1742
Non-polymers6874
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-32 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.922, 173.922, 97.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CPB / 2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE / FLAVOPIRIDOL / Alvocidib


Mass: 401.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClNO5 / Comment: inhibitor, alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M NaK phosphate, 20% PEG 1000, 0.2M NaCl, 4mM TCEP, 0.1mM Flavopiridol , pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.8→38.378 Å / Num. all: 26960 / Num. obs: 26960 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.955.80.5851.22277039430.585100
2.95-3.135.80.3342.12158437320.334100
3.13-3.355.80.193.72037035250.19100
3.35-3.615.80.1245.51883932630.124100
3.61-3.965.80.0947.11718929810.094100
3.96-4.435.70.07881580327510.078100
4.43-5.115.70.0797.81355623790.079100
5.11-6.265.60.0976.21138420170.09799.8
6.26-8.855.40.077.8830515510.07100
8.85-59.555.30.0649.543638180.06495.4

-
Processing

Software
NameClassification
ProDCdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BLH
Resolution: 2.8→36.96 Å / FOM work R set: 0.84 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2699 5.02 %RANDOM
Rwork0.176 ---
all-26960 --
obs-26956 99.55 %-
Solvent computationBsol: 50.12 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso max: 223.93 Å2 / Biso mean: 89.79 Å2 / Biso min: 39.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.301 Å2-0 Å2-0 Å2
2--1.301 Å20 Å2
3----2.602 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 43 20 4551
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.661
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.0491
X-RAY DIFFRACTIONf_dihedral_angle_d10.3031
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0751
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.8-2.8090.243471X-RAY DIFFRACTION10295
2.809-2.8190.275543X-RAY DIFFRACTION10297
2.819-2.8280.272510X-RAY DIFFRACTION10292
2.828-2.8380.258492X-RAY DIFFRACTION10293
2.838-2.8470.257556X-RAY DIFFRACTION10294
2.847-2.8570.249444X-RAY DIFFRACTION10293
2.857-2.8670.254507X-RAY DIFFRACTION10294
2.867-2.8770.266469X-RAY DIFFRACTION10295
2.877-2.8880.238530X-RAY DIFFRACTION10297
2.888-2.8980.245483X-RAY DIFFRACTION10294
2.898-2.9080.271526X-RAY DIFFRACTION10299
2.908-2.9190.262519X-RAY DIFFRACTION10296
2.919-2.930.261556X-RAY DIFFRACTION10293
2.93-2.9410.241448X-RAY DIFFRACTION10295
2.941-2.9520.255459X-RAY DIFFRACTION10294
2.952-2.9640.239486X-RAY DIFFRACTION10294
2.964-2.9750.244525X-RAY DIFFRACTION10293
2.975-2.9870.231540X-RAY DIFFRACTION10296
2.987-2.9990.232457X-RAY DIFFRACTION10295
2.999-3.0110.244546X-RAY DIFFRACTION10296
3.011-3.0240.22480X-RAY DIFFRACTION10295
3.024-3.0360.244518X-RAY DIFFRACTION10295
3.036-3.0490.235446X-RAY DIFFRACTION10294
3.049-3.0620.221507X-RAY DIFFRACTION10295
3.062-3.0750.218549X-RAY DIFFRACTION10296
3.075-3.0880.216488X-RAY DIFFRACTION10296
3.088-3.1020.222506X-RAY DIFFRACTION10293
3.102-3.1160.221513X-RAY DIFFRACTION10294
3.116-3.130.215460X-RAY DIFFRACTION10295
3.13-3.1450.205574X-RAY DIFFRACTION10295
3.145-3.1590.2422X-RAY DIFFRACTION10294
3.159-3.1740.194531X-RAY DIFFRACTION10294
3.174-3.190.225462X-RAY DIFFRACTION10295
3.19-3.2050.218533X-RAY DIFFRACTION10294
3.205-3.2210.217551X-RAY DIFFRACTION10294
3.221-3.2370.207428X-RAY DIFFRACTION10295
3.237-3.2530.206484X-RAY DIFFRACTION10295
3.253-3.270.205552X-RAY DIFFRACTION10296
3.27-3.2880.215507X-RAY DIFFRACTION10296
3.288-3.3050.196535X-RAY DIFFRACTION10298
3.305-3.3230.197468X-RAY DIFFRACTION10295
3.323-3.3420.209539X-RAY DIFFRACTION10296
3.342-3.360.194427X-RAY DIFFRACTION10294
3.36-3.3790.18551X-RAY DIFFRACTION10296
3.379-3.3990.198498X-RAY DIFFRACTION10294
3.399-3.4190.185511X-RAY DIFFRACTION10295
3.419-3.440.181490X-RAY DIFFRACTION10295
3.44-3.4610.196501X-RAY DIFFRACTION10295
3.461-3.4820.181505X-RAY DIFFRACTION10295
3.482-3.5050.208518X-RAY DIFFRACTION10296
3.505-3.5270.189493X-RAY DIFFRACTION10293
3.527-3.5510.185468X-RAY DIFFRACTION10292
3.551-3.5750.187472X-RAY DIFFRACTION10291
3.575-3.5990.175516X-RAY DIFFRACTION10293
3.599-3.6250.196557X-RAY DIFFRACTION10296
3.625-3.6510.175460X-RAY DIFFRACTION10295
3.651-3.6770.174509X-RAY DIFFRACTION10295
3.677-3.7050.173500X-RAY DIFFRACTION10294
3.705-3.7340.164490X-RAY DIFFRACTION10294
3.734-3.7630.176509X-RAY DIFFRACTION10294
3.763-3.7930.173473X-RAY DIFFRACTION10297
3.793-3.8250.157530X-RAY DIFFRACTION10295
3.825-3.8570.163516X-RAY DIFFRACTION10296
3.857-3.890.167513X-RAY DIFFRACTION10294
3.89-3.9250.162464X-RAY DIFFRACTION10294
3.925-3.9610.161498X-RAY DIFFRACTION10297
3.961-3.9980.15542X-RAY DIFFRACTION10295
3.998-4.0370.157476X-RAY DIFFRACTION10294
4.037-4.0770.143505X-RAY DIFFRACTION10293
4.077-4.120.136486X-RAY DIFFRACTION10294
4.12-4.1630.133497X-RAY DIFFRACTION10294
4.163-4.2090.147534X-RAY DIFFRACTION10295
4.209-4.2570.132479X-RAY DIFFRACTION10297
4.257-4.3070.14489X-RAY DIFFRACTION10296
4.307-4.3590.135492X-RAY DIFFRACTION10295
4.359-4.4140.124586X-RAY DIFFRACTION10296
4.414-4.4720.127443X-RAY DIFFRACTION10296
4.472-4.5330.136518X-RAY DIFFRACTION10294
4.533-4.5980.137512X-RAY DIFFRACTION10296
4.598-4.6670.129486X-RAY DIFFRACTION10293
4.667-4.7390.14486X-RAY DIFFRACTION10293
4.739-4.8170.117513X-RAY DIFFRACTION10294
4.817-4.90.126480X-RAY DIFFRACTION10297
4.9-4.9890.121534X-RAY DIFFRACTION10295
4.989-5.0840.126472X-RAY DIFFRACTION10296
5.084-5.1880.129494X-RAY DIFFRACTION10291
5.188-5.30.134516X-RAY DIFFRACTION10295
5.3-5.4230.149512X-RAY DIFFRACTION10295
5.423-5.5580.136494X-RAY DIFFRACTION10295
5.558-5.7080.16518X-RAY DIFFRACTION10297
5.708-5.8760.159477X-RAY DIFFRACTION10293
5.876-6.0640.163499X-RAY DIFFRACTION10294
6.064-6.280.185499X-RAY DIFFRACTION10294
6.28-6.530.182507X-RAY DIFFRACTION10296
6.53-6.8260.173474X-RAY DIFFRACTION10292
6.826-7.1830.162491X-RAY DIFFRACTION10295
7.183-7.6290.16520X-RAY DIFFRACTION10295
7.629-8.2120.139504X-RAY DIFFRACTION10294
8.212-9.0280.13502X-RAY DIFFRACTION10296
9.028-10.310.116495X-RAY DIFFRACTION10294
10.31-12.8970.13464X-RAY DIFFRACTION10288
12.897-36.960.256461X-RAY DIFFRACTION10286
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1558-0.04810.23082.32520.16581.79150.2850.1592-0.34810.4787-0.26280.0850.5758-0.0003-0.01050.4702-0.0968-0.09150.38860.01450.55147.9636-17.5831-2.0273
22.1264-0.4559-0.221.08890.10261.40840.12680.07990.20130.1104-0.071-0.3659-0.10290.0886-0.0450.3344-0.0381-0.10930.4676-0.06060.437521.43533.7177-20.7099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA7 - 326
2X-RAY DIFFRACTION2chain BB9 - 259

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more