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- PDB-4nst: Crystal structure of human Cdk12/Cyclin K in complex with ADP-alu... -

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Basic information

Entry
Database: PDB / ID: 4nst
TitleCrystal structure of human Cdk12/Cyclin K in complex with ADP-aluminum fluoride
Components
  • Cyclin-K
  • Cyclin-dependent kinase 12
KeywordsTRANSFERASE/TRANSCRIPTION / transcription / RNA polymerase II / phosphorylation / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / 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 / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / 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 / RNA polymerase II transcribes snRNA genes / regulation of signal transduction / 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 / RNA Polymerase II Pre-transcription Events / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / transcription by RNA polymerase II / protein autophosphorylation / protein kinase activity / nuclear speck / cell cycle / cell division / protein serine kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Haspin like kinase 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 ...Cyclin-T2-like, C-terminal domain / Haspin like kinase 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 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBoesken, C.A. / Farnung, L. / Anand, K. / Geyer, M.
CitationJournal: Nat Commun / Year: 2014
Title: The structure and substrate specificity of human Cdk12/Cyclin K.
Authors: Bosken, C.A. / Farnung, L. / Hintermair, C. / Merzel Schachter, M. / Vogel-Bachmayr, K. / Blazek, D. / Anand, K. / Fisher, R.P. / Eick, D. / Geyer, M.
History
DepositionNov 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 12
B: Cyclin-K
C: Cyclin-dependent kinase 12
D: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,82919
Polymers144,3884
Non-polymers1,44115
Water7,080393
1
A: Cyclin-dependent kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4117
Polymers40,7651
Non-polymers6466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4912
Polymers31,4291
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cyclin-dependent kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3876
Polymers40,7651
Non-polymers6225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5404
Polymers31,4291
Non-polymers1113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.720, 78.850, 91.490
Angle α, β, γ (deg.)104.04, 85.76, 101.46
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 718:760 or resseq 764:796 or resseq...
211chain C and (resseq 718:760 or resseq 764:796 or resseq...
112chain B and (resseq 21:227 or resseq 233:261 )
212chain D and (resseq 21:227 or resseq 233:261 )

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Cyclin-dependent kinase 12 / / Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 ...Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 / CDC2-related protein kinase 7 / Cell division protein kinase 12 / hCDK12


Mass: 40764.992 Da / Num. of mol.: 2 / Fragment: Protein kinase domain, residues 714-1063
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK12, CRK7, CRKRS, KIAA0904 / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-K


Mass: 31429.172 Da / Num. of mol.: 2 / Fragment: UNP residues 1-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Plasmid: pIDK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: O75909

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Non-polymers , 5 types, 408 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / Aluminium 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.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→48.7 Å / Num. all: 65263 / Num. obs: 65263 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.52 Å2
Reflection shellResolution: 2.2→2.25 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLQ, 2I53

3blq

2i53


Resolution: 2.2→48.711 Å / SU ML: 0.38 / σ(F): 2 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 3261 5 %
Rwork0.1952 --
obs0.1975 65227 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.684 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5687 Å2-4.9309 Å27.2874 Å2
2---0.2857 Å2-6.6293 Å2
3----6.283 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 85 393 9618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159455
X-RAY DIFFRACTIONf_angle_d1.63112811
X-RAY DIFFRACTIONf_dihedral_angle_d20.9663485
X-RAY DIFFRACTIONf_chiral_restr0.1321390
X-RAY DIFFRACTIONf_plane_restr0.0071618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2464X-RAY DIFFRACTIONPOSITIONAL
12C2464X-RAY DIFFRACTIONPOSITIONAL0.094
21B1919X-RAY DIFFRACTIONPOSITIONAL
22D1919X-RAY DIFFRACTIONPOSITIONAL0.102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23280.31671430.23972701X-RAY DIFFRACTION97
2.2328-2.26770.26961420.21212695X-RAY DIFFRACTION97
2.2677-2.30490.25631390.19992666X-RAY DIFFRACTION97
2.3049-2.34470.27041440.2162734X-RAY DIFFRACTION97
2.3447-2.38730.31081410.22542685X-RAY DIFFRACTION97
2.3873-2.43320.29531400.2112646X-RAY DIFFRACTION97
2.4332-2.48290.25991440.20592749X-RAY DIFFRACTION97
2.4829-2.53690.28541400.21472663X-RAY DIFFRACTION97
2.5369-2.59590.30261440.20982735X-RAY DIFFRACTION97
2.5959-2.66080.28721400.21432658X-RAY DIFFRACTION97
2.6608-2.73270.30471420.2172715X-RAY DIFFRACTION97
2.7327-2.81310.25891410.20892688X-RAY DIFFRACTION97
2.8131-2.90390.25881430.2052716X-RAY DIFFRACTION98
2.9039-3.00770.26051410.2082666X-RAY DIFFRACTION97
3.0077-3.12810.27611420.20772708X-RAY DIFFRACTION97
3.1281-3.27040.26911420.20232695X-RAY DIFFRACTION97
3.2704-3.44280.23541400.18552663X-RAY DIFFRACTION97
3.4428-3.65840.22431420.17492691X-RAY DIFFRACTION97
3.6584-3.94080.20431430.16512711X-RAY DIFFRACTION97
3.9408-4.33720.20151400.15132661X-RAY DIFFRACTION97
4.3372-4.96420.18121430.15242729X-RAY DIFFRACTION98
4.9642-6.25230.19331430.17382707X-RAY DIFFRACTION98
6.2523-48.7230.15221420.16252684X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -10.2535 Å / Origin y: -26.3036 Å / Origin z: -2.7411 Å
111213212223313233
T0.118 Å20.012 Å2-0.0124 Å2-0.1383 Å20.0004 Å2--0.1423 Å2
L0.1076 °20.0514 °2-0.1947 °2-0.0455 °2-0.0584 °2--0.3345 °2
S0.0017 Å °-0.02 Å °0.0214 Å °-0.0201 Å °0.0165 Å °0 Å °0.0314 Å °0.0116 Å °-0 Å °
Refinement TLS groupSelection details: all

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