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- PDB-1jkw: STRUCTURE OF CYCLIN MCS2 -

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Basic information

Entry
Database: PDB / ID: 1jkw
TitleSTRUCTURE OF CYCLIN MCS2
ComponentsCYCLIN H
KeywordsCELL DIVISION / CYCLIN / CELL CYCLE / NUCLEAR PROTEIN
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme 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 ...cyclin-dependent protein kinase activating kinase holoenzyme 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 / Formation of RNA Pol II elongation complex / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / 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 / transcription by RNA polymerase II / protein stabilization / cell cycle / 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
AuthorsAndersen, G. / Poterszman, A. / Moras, D. / Thierry, J.C.
Citation
Journal: FEBS Lett. / Year: 1996
Title: The crystal structure of human cyclin H.
Authors: Andersen, G. / Poterszman, A. / Egly, J.M. / Moras, D. / Thierry, J.C.
#1: Journal: To be Published
Title: Expression in Escherichia Coli: Purification and Characterisation of Cyclin H, a Subunit of Human General Transcription/ DNA Repair Factor Tfiih
Authors: Poterszman, A. / Andersen, G. / Busso, D. / Rossignol, M. / Egly, J.M. / Thierry, J.C.
#2: Journal: Structure / Year: 1995
Title: The Crystal Structure of Cyclin A
Authors: Brown, N.R. / Noble, M.E. / Endicott, J.A. / Garman, E.F. / Wakatsuki, S. / Mitchell, E. / Rasmussen, B. / Hunt, T. / Johnson, L.N.
#3: Journal: Nature / Year: 1995
Title: Mechanism of Cdk Activation Revealed by the Structure of a Cyclina-Cdk2 Complex
Authors: Jeffrey, P.D. / Russo, A.A. / Polyak, K. / Gibbs, E. / Hurwitz, J. / Massague, J. / Pavletich, N.P.
History
DepositionOct 11, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)37,6811
Polymers37,6811
Non-polymers00
Water91951
1
A: CYCLIN H

A: CYCLIN H


Theoretical massNumber of molelcules
Total (without water)75,3632
Polymers75,3632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)84.060, 84.060, 373.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein CYCLIN H / RCYCLIN H (RECOMBINANT)


Mass: 37681.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HIS-TAG REMOVED BY THROMBIN DIGESTION / Gene: HUMAN CYCLIN H / Plasmid: PET15B / Gene (production host): HUMAN CYCLIN H / Production host: Escherichia coli (E. coli) / References: UniProt: P51946
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 4.37 Å3/Da / Density % sol: 72 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Mammonium phosphate1reservoir
20.1 Msodium citrate1reservoir
32 %glycerol1reservoir
410 mMbeta-ME1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionNum. obs: 20809 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Num. measured all: 21133

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.6→14 Å / σ(F): 2
Details: THE LOOP LEU 236 - THR 243 HAS LIMITED DENSITY, AND IS NOT VERY RELIABLE.
RfactorNum. reflection
Rfree0.272 -
Rwork0.222 -
obs0.222 18836
Displacement parametersBiso mean: 55.9 Å2
Refine analyzeLuzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 0 51 2349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.86
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

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