[English] 日本語
Yorodumi
- PDB-3tni: structure of CDK9/cyclin T F241L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tni
Titlestructure of CDK9/cyclin T F241L
Components
  • Cyclin-T1
  • Cyclin-dependent kinase 9
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / cyclin dependent kinase / Kinase / cyclin / phosphotransfer / CDK-cyclin complex / phosphorylated on threonine 186 / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / positive regulation of DNA-templated transcription, elongation / negative regulation of protein localization to chromatin / [RNA-polymerase]-subunit kinase / transcription elongation-coupled chromatin remodeling / replication fork processing / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / 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 / protein serine kinase activity / DNA repair / 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
Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 3.234 Å
AuthorsBaumli, S. / Hole, A.J. / Endicott, J.A.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: The CDK9 C-helix Exhibits Conformational Plasticity That May Explain the Selectivity of CAN508.
Authors: Baumli, S. / Hole, A.J. / Noble, M.E. / Endicott, J.A.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclin-dependent kinase 9
B: Cyclin-T1


Theoretical massNumber of molelcules
Total (without water)68,1942
Polymers68,1942
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.610, 173.610, 97.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsdimer

-
Components

#1: Protein Cyclin-dependent kinase 9 / / C-2K / Cell division cycle 2-like protein kinase 4 / Cell division protein kinase 9 / ...C-2K / Cell division cycle 2-like protein kinase 4 / Cell division protein kinase 9 / Serine/threonine-protein kinase PITALRE


Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 2-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC2L4, CDK9 / Plasmid: pVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / CycT1 / Cyclin-T


Mass: 30139.453 Da / Num. of mol.: 1 / Fragment: cyclin boxes, UNP residues 1-259 / Mutation: F241L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Plasmid: pVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60563

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 8% PEG1K, 600mM NaCL, 100mM Na/K phosphate, 4mM TCEP, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2011
RadiationMonochromator: Accel fixed exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.234→59.527 Å / Num. all: 17300 / Num. obs: 17300 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.07 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.23-3.413.50.4891.6883025570.48999.7
3.41-3.623.40.3092.4835224240.30999.5
3.62-3.873.50.2043.7785522260.20499.3
3.87-4.173.30.1196694420940.11999.1
4.17-4.573.30.0858.1639619310.08598
4.57-5.113.40.0759578417120.07597.8
5.11-5.93.30.0699.8510515390.06998.8
5.9-7.233.50.05313.1446312890.05398.6
7.23-10.233.20.04114.832189910.04197.8
10.23-81.7873.40.03217.818225370.03296.4

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
xia2data scaling
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: Rigid body refinement / Resolution: 3.234→49.093 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8541 / SU ML: 0.7 / σ(F): 1.96 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 867 5.01 %copied from 3BLH
Rwork0.1633 ---
all0.1657 17503 --
obs0.1657 17290 98.78 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.375 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 279.81 Å2 / Biso mean: 123.6758 Å2 / Biso min: 48.29 Å2
Baniso -1Baniso -2Baniso -3
1--11.7647 Å2-0 Å20 Å2
2---11.7647 Å2-0 Å2
3---23.5294 Å2
Refinement stepCycle: LAST / Resolution: 3.234→49.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 0 0 4489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094589
X-RAY DIFFRACTIONf_angle_d1.3446223
X-RAY DIFFRACTIONf_chiral_restr0.099702
X-RAY DIFFRACTIONf_plane_restr0.007786
X-RAY DIFFRACTIONf_dihedral_angle_d13.6361717
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2342-3.43680.30971270.24227802907100
3.4368-3.7020.24151600.2022737289799
3.702-4.07440.22821480.16482751289999
4.0744-4.66360.15551320.12892712284498
4.6636-5.87410.19361500.13772727287799
5.8741-49.09840.21631500.17242716286698
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)
14.81430.0744-0.38851.63080.38844.81150.27430.423-0.4788-0.45370.0808-0.42870.27710.4075-0.2890.750.07430.06850.8723-0.11550.944747.52-11.6228-20.692
22.0576-1.47621.01575.7177-0.1274.04710.2071-0.3382-0.64681.2974-0.07590.02751.2387-0.0102-0.1361.358-0.1274-0.14330.77630.12671.03946.62-20.29466.9682
34.6681-0.2932-0.8143.68680.38312.6891-0.0450.11110.41280.04950.0204-0.2473-0.1956-0.11840.01170.5184-0.0598-0.1080.6839-0.00390.388221.71433.572-20.5198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:105)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 106:330)A0
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:259)B0

+
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