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- PDB-2y1x: CRYSTAL STRUCTURE OF COACTIVATOR ASSOCIATED ARGININE METHYLTRANSF... -

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Basic information

Entry
Database: PDB / ID: 2y1x
TitleCRYSTAL STRUCTURE OF COACTIVATOR ASSOCIATED ARGININE METHYLTRANSFERASE 1 (CARM1) IN COMPLEX WITH SINEFUNGIN AND INDOLE INHIBITOR
ComponentsHISTONE-ARGININE METHYLTRANSFERASE CARM1
KeywordsTRANSFERASE / HISTONE MODIFICATION
Function / homology
Function and homology information


: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / RMTs methylate histone arginines / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-845 / S-ADENOSYL-L-HOMOCYSTEINE / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSack, J.S. / Thieffine, S. / Bandiera, T. / Fasolini, M. / Duke, G.J. / Jayaraman, L. / Kish, K.F. / Klei, H.E. / Purandare, A.V. / Rosettani, P. ...Sack, J.S. / Thieffine, S. / Bandiera, T. / Fasolini, M. / Duke, G.J. / Jayaraman, L. / Kish, K.F. / Klei, H.E. / Purandare, A.V. / Rosettani, P. / Troiani, S. / Xie, D. / Bertrand, J.A.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural Basis for Carm1 Inhibition by Indole and Pyrazole Inhibitors
Authors: Sack, J.S. / Thieffine, S. / Bandiera, T. / Fasolini, M. / Duke, G.J. / Jayaraman, L. / Kish, K.F. / Klei, H.E. / Purandare, A.V. / Rosettani, P. / Troiani, S. / Xie, D. / Bertrand, J.A.
History
DepositionDec 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE-ARGININE METHYLTRANSFERASE CARM1
B: HISTONE-ARGININE METHYLTRANSFERASE CARM1
C: HISTONE-ARGININE METHYLTRANSFERASE CARM1
D: HISTONE-ARGININE METHYLTRANSFERASE CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,58916
Polymers157,9204
Non-polymers3,66912
Water8,287460
1
B: HISTONE-ARGININE METHYLTRANSFERASE CARM1
D: HISTONE-ARGININE METHYLTRANSFERASE CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7948
Polymers78,9602
Non-polymers1,8356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-43.6 kcal/mol
Surface area25370 Å2
MethodPISA
2
A: HISTONE-ARGININE METHYLTRANSFERASE CARM1
C: HISTONE-ARGININE METHYLTRANSFERASE CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7948
Polymers78,9602
Non-polymers1,8356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-43.9 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.558, 98.757, 207.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
HISTONE-ARGININE METHYLTRANSFERASE CARM1 / CARM1 / COACTIVATOR-ASSOCIATED ARGININE METHYLTRANSFERASE 1 / PROTEIN ARGININE N-METHYLTRANSFERASE 4


Mass: 39479.910 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 135-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MM294(DE3) / References: UniProt: Q86X55, EC: 2.1.1.125
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-845 / N-(3-{5-[5-(1H-INDOL-4-YL)-1,3,4-OXADIAZOL-2-YL]-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL}BENZYL)-L-ALANINAMIDE


Mass: 497.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H22F3N7O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.5 Å3/Da / Density % sol: 50.1 % / Description: NONE
Crystal growpH: 8.5
Details: 20-30% PEG 2000K, 0.1 M TRIS-HCL PH 8.5, 0.2 M TRIMETHYLAMINE N-OXIDE DIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 61230 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.41
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNX2005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERNAL STRUCTURE OF CARM1

Resolution: 2.4→29.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2727506.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3057 5 %RANDOM
Rwork0.207 ---
obs0.21 61211 99.3 %-
all-61211 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1039 Å2 / ksol: 0.320394 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.84 Å20 Å20 Å2
2---0.48 Å20 Å2
3----8.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10980 0 252 460 11692
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 470 4.7 %
Rwork0.287 9633 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4293.PAR293.TOP
X-RAY DIFFRACTION5SAH.PARSAH.TOP

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