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- PDB-5efq: Crystal structure of human Cdk13/Cyclin K in complex with ADP-alu... -

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Basic information

Entry
Database: PDB / ID: 5efq
TitleCrystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride
Components
  • Cyclin-K
  • Cyclin-dependent kinase 13
KeywordsTRANSFERASE / kinase / cyclin / ADP
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / alternative mRNA splicing, via spliceosome / negative regulation of stem cell differentiation / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / alternative mRNA splicing, via spliceosome / negative regulation of stem cell differentiation / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / regulation of cyclin-dependent protein serine/threonine kinase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / hemopoiesis / RNA polymerase II transcribes snRNA genes / regulation of signal transduction / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / ficolin-1-rich granule lumen / transcription by RNA polymerase II / protein kinase activity / nuclear speck / cell division / protein serine kinase activity / DNA damage response / Neutrophil degranulation / regulation of transcription by RNA polymerase II / protein kinase binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Cyclin, C-terminal domain / Cyclin_C / 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 / Cyclin, C-terminal domain / Cyclin_C / 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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Cyclin-K / Cyclin-dependent kinase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHoenig, D. / Greifenberg, A.K. / Anand, K. / Geyer, M.
CitationJournal: Cell Rep / Year: 2016
Title: Structural and Functional Analysis of the Cdk13/Cyclin K Complex.
Authors: Greifenberg, A.K. / Honig, D. / Pilarova, K. / Duster, R. / Bartholomeeusen, K. / Bosken, C.A. / Anand, K. / Blazek, D. / Geyer, M.
History
DepositionOct 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Jan 10, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Oct 23, 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: Cyclin-dependent kinase 13
B: Cyclin-K
C: Cyclin-dependent kinase 13
D: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,02212
Polymers143,9024
Non-polymers1,1208
Water5,206289
1
A: Cyclin-dependent kinase 13
B: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5116
Polymers71,9512
Non-polymers5604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cyclin-dependent kinase 13
D: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5116
Polymers71,9512
Non-polymers5604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.780, 81.820, 93.140
Angle α, β, γ (deg.)74.08, 84.26, 76.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Cyclin-dependent kinase 13 / CDC2-related protein kinase 5 / Cell division cycle 2-like protein kinase 5 / Cell division protein ...CDC2-related protein kinase 5 / Cell division cycle 2-like protein kinase 5 / Cell division protein kinase 13 / hCDK13 / Cholinesterase-related cell division controller


Mass: 40521.863 Da / Num. of mol.: 2 / Fragment: UNP residues 694-1039
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK13, CDC2L, CDC2L5, CHED, KIAA1791 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q14004, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-K


Mass: 31429.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75909

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Non-polymers , 4 types, 297 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 25.5% PEG 3350, 0.35 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→49.4 Å / Num. obs: 90134 / % possible obs: 96 % / Redundancy: 1 % / Net I/σ(I): 13
Reflection shellMean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NST

4nst


Resolution: 2→46.186 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 4489 5 %
Rwork0.1939 --
obs0.1966 89772 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8998 0 66 289 9353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099296
X-RAY DIFFRACTIONf_angle_d1.12112635
X-RAY DIFFRACTIONf_dihedral_angle_d15.1263405
X-RAY DIFFRACTIONf_chiral_restr0.0491383
X-RAY DIFFRACTIONf_plane_restr0.0061598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.02290.44421040.40961970X-RAY DIFFRACTION66
2.0229-2.04670.43361540.37372857X-RAY DIFFRACTION95
2.0467-2.07170.41381480.36152787X-RAY DIFFRACTION94
2.0717-2.09790.35511500.34372914X-RAY DIFFRACTION96
2.0979-2.12550.3791520.32392811X-RAY DIFFRACTION95
2.1255-2.15460.39821490.30882830X-RAY DIFFRACTION95
2.1546-2.18540.38971480.29632830X-RAY DIFFRACTION95
2.1854-2.2180.3881540.2822917X-RAY DIFFRACTION95
2.218-2.25270.34691470.27132818X-RAY DIFFRACTION95
2.2527-2.28960.321520.25422860X-RAY DIFFRACTION96
2.2896-2.32910.35241500.2512870X-RAY DIFFRACTION95
2.3291-2.37140.34851490.23512843X-RAY DIFFRACTION96
2.3714-2.41710.31161550.23122917X-RAY DIFFRACTION95
2.4171-2.46640.31751490.2332869X-RAY DIFFRACTION96
2.4664-2.520.33461510.24362885X-RAY DIFFRACTION96
2.52-2.57860.34951490.24242879X-RAY DIFFRACTION96
2.5786-2.64310.32141530.23262906X-RAY DIFFRACTION97
2.6431-2.71460.29691530.22032889X-RAY DIFFRACTION97
2.7146-2.79440.26841540.21712925X-RAY DIFFRACTION97
2.7944-2.88460.28111530.23172905X-RAY DIFFRACTION97
2.8846-2.98770.26681530.22532955X-RAY DIFFRACTION97
2.9877-3.10730.30161520.21542884X-RAY DIFFRACTION97
3.1073-3.24870.23881510.20522882X-RAY DIFFRACTION96
3.2487-3.41990.26411450.19892876X-RAY DIFFRACTION95
3.4199-3.63410.22881500.18442876X-RAY DIFFRACTION95
3.6341-3.91460.20371560.16652886X-RAY DIFFRACTION96
3.9146-4.30820.20251510.14362836X-RAY DIFFRACTION96
4.3082-4.9310.17981520.13882832X-RAY DIFFRACTION94
4.931-6.21020.20831540.16342904X-RAY DIFFRACTION96
6.2102-46.19810.18871510.15442870X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 10.0073 Å / Origin y: -26.8098 Å / Origin z: 3.2096 Å
111213212223313233
T0.2565 Å2-0.0444 Å2-0.0333 Å2-0.4176 Å20.0347 Å2--0.4081 Å2
L0.1114 °2-0.2239 °2-0.6143 °2-0.3233 °20.4464 °2--1.6941 °2
S0.059 Å °0.0635 Å °0.0334 Å °0.0369 Å °0.0099 Å °0.0396 Å °-0.0459 Å °-0.16 Å °-0.062 Å °
Refinement TLS groupSelection details: all

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