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- PDB-2j8a: X-ray structure of the N-terminus RRM domain of Set1 -

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Basic information

Entry
Database: PDB / ID: 2j8a
TitleX-ray structure of the N-terminus RRM domain of Set1
ComponentsHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC
KeywordsTRANSFERASE / HISTONE METHYLTRANSFERASE / RRM FOLD / TELOMERE / NUCLEAR PROTEIN / METHYLTRANSFERASE / CHROMOSOMAL PROTEIN
Function / homology
Function and homology information


positive regulation of synaptonemal complex assembly / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / meiotic DNA double-strand break formation / sterol homeostasis / ascospore formation / [histone H3]-lysine4 N-trimethyltransferase / synaptonemal complex assembly / regulation of chromatin organization ...positive regulation of synaptonemal complex assembly / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / meiotic DNA double-strand break formation / sterol homeostasis / ascospore formation / [histone H3]-lysine4 N-trimethyltransferase / synaptonemal complex assembly / regulation of chromatin organization / histone H3K4 trimethyltransferase activity / protein methylation / rDNA heterochromatin formation / Set1C/COMPASS complex / protein-lysine N-methyltransferase activity / histone H3K4 methyltransferase activity / silent mating-type cassette heterochromatin formation / cellular response to stress / subtelomeric heterochromatin formation / telomere maintenance / chromosome, telomeric region / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N ...Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / RRM (RNA recognition motif) domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase, H3 lysine-4 specific
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å
AuthorsTresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. ...Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / Tordera, V. / Zinn-Justin, S. / Chavez, S. / Van Tilbeurgh, H. / Geli, V.
Citation
Journal: To be Published
Title: X-Ray Structure of the N-Terminus Rrm Domain of Set1
Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / ...Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / Tordera, V. / Zinn-Justin, S. / Chavez, S. / Van Tilbeurgh, H. / Geli, V.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Structural Characterization of Set1 RNA Recognition Motifs and Their Role in Histone H3 Lysine 4 Methylation.
Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / ...Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / Tordera, V. / Zinn-Justin, S. / Chavez, S. / Van Tilbeurgh, H. / Geli, V.
History
DepositionOct 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC


Theoretical massNumber of molelcules
Total (without water)15,5691
Polymers15,5691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.790, 123.790, 123.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC / COMPASS COMPONENT SET1 / SET DOMAIN-CONTAINING PROTEIN 1 / SET1 HISTONE METHYLTRANSFERASE


Mass: 15568.778 Da / Num. of mol.: 1 / Fragment: N-TERMINUS RRM DOMAIN, RESIDUES 247-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S228C / Plasmid: PET-9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD
References: UniProt: P38827, histone-lysine N-methyltransferase

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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: 5.67 Å3/Da / Density % sol: 75.2 %
Crystal growpH: 4.6
Details: 2.15M AMMONIUM SULFATE,50MM NACITRATE PH4.6,4% POLYPROPYLENE-GLYCOL 400,3% GLYCEROL, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→39.5 Å / Num. obs: 7192 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 23.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.12 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 302-306 AND 367-CTERMINUS ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 321 4.8 %RANDOM
Rwork0.246 ---
obs0.247 6381 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.85 Å2
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 0 0 915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0540.022933
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.0971.9431255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8325112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87925.58143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.17915173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.192151
X-RAY DIFFRACTIONr_chiral_restr0.3350.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02685
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3480.2520
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3920.2651
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2731.5586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5632919
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0783403
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7414.5336
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.07 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.43 23
Rwork0.366 443

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