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- PDB-1kxu: CYCLIN H, A POSITIVE REGULATORY SUBUNIT OF CDK ACTIVATING KINASE -

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Basic information

Entry
Database: PDB / ID: 1kxu
TitleCYCLIN H, A POSITIVE REGULATORY SUBUNIT OF CDK ACTIVATING KINASE
ComponentsCYCLIN H
KeywordsREGULATORY PROTEIN / CYCLIN / CELL CYCLE / CELL DIVISION / NUCLEAR PROTEIN / ALPHA-HELICAL STRUCTURE
Function / homology
Function and homology information


CAK-ERCC2 complex / transcription factor TFIIK complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex ...CAK-ERCC2 complex / transcription factor TFIIK complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / Formation of RNA Pol II elongation complex / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein stabilization / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
CyclinH/Ccl1 / Cyclin, C-terminal domain 2 / Cyclin C-terminal 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 ...CyclinH/Ccl1 / Cyclin, C-terminal domain 2 / Cyclin C-terminal 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKim, K.K. / Chamberin, H.M. / Morgan, D.O. / Kim, S.-H.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Three-dimensional structure of human cyclin H, a positive regulator of the CDK-activating kinase.
Authors: Kim, K.K. / Chamberlin, H.M. / Morgan, D.O. / Kim, S.H.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: A Novel Cyclin Associates with Mo15/Cdk7 to Form the Cdk-Activating Kinase
Authors: Fisher, R.P. / Morgan, D.O.
History
DepositionAug 8, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLIN H


Theoretical massNumber of molelcules
Total (without water)38,8871
Polymers38,8871
Non-polymers00
Water2,486138
1
A: CYCLIN H

A: CYCLIN H


Theoretical massNumber of molelcules
Total (without water)77,7742
Polymers77,7742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
Unit cell
Length a, b, c (Å)84.080, 84.080, 374.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-382-

HOH

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Components

#1: Protein CYCLIN H


Mass: 38886.754 Da / Num. of mol.: 1 / Mutation: INS(MSHHHHHHGS-M1) (HISTIDINE TAG)
Source method: isolated from a genetically manipulated source
Details: A POSITIVE REGULATORY SUBUNIT OF CDK-ACTIVATING KINASE
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELL / Plasmid: BACULOVIRUS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 75 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlcyclin H1drop
2200 mMsodium chloride1drop
310 %(v/v)glycerol1drop
41 mMEDTA1drop
51 mMDTT1drop
610 mMHEPES1drop
7800 mMlithium sulohate1drop
8400 mMammonium sulphate1drop
9100 mMcitrate1drop
10800 mMlithium sulohate1reservoir
11400 mMammonium sulphate1reservoir
12100 mMcitrate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.1
DetectorType: FUJI FILM / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 21, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionNum. obs: 18913 / % possible obs: 85.7 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. measured all: 71856 / Rmerge(I) obs: 0.048

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.295 -
Rwork0.214 -
obs0.214 17904
Displacement parametersBiso mean: 46.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 0 138 2349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16141 / Num. reflection Rfree: 1763
Solvent computation
*PLUS
Displacement parameters
*PLUS

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