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- PDB-3b3g: The 2.4 A crystal structure of the apo catalytic domain of coacti... -

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Basic information

Entry
Database: PDB / ID: 3b3g
TitleThe 2.4 A crystal structure of the apo catalytic domain of coactivator-associated arginine methyl transferase I(CARM1,140-480).
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE / CATALYTIC DOMAIN / Chromatin regulator / mRNA processing / mRNA splicing / Nucleus / S-adenosyl-L-methionine / Transcription / Transcription regulation
Function / homology
Function and homology information


RMTs methylate histone arginines / Estrogen-dependent gene expression / Regulation of lipid metabolism by PPARalpha / histone H3R26 methyltransferase activity / Cytoprotection by HMOX1 / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / negative regulation of dendrite development ...RMTs methylate histone arginines / Estrogen-dependent gene expression / Regulation of lipid metabolism by PPARalpha / histone H3R26 methyltransferase activity / Cytoprotection by HMOX1 / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / 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 / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / intracellular estrogen receptor signaling pathway / intracellular steroid hormone receptor signaling pathway / response to cAMP / protein localization to chromatin / RNA splicing / nuclear receptor coactivator activity / lysine-acetylated histone binding / mRNA processing / RNA polymerase II transcription regulator complex / methylation / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / 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
Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTroffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J.
Citation
Journal: Embo J. / Year: 2007
Title: Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains.
Authors: Troffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, purification, crystallization and preliminary crystallographic study of isolated modules of the mouse coactivator-associated arginine methyltransferase 1.
Authors: Troffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J.
History
DepositionOct 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)77,5482
Polymers77,5482
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.817, 98.116, 207.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Histone-arginine methyltransferase CARM1 / Protein arginine N-methyltransferase 4 / Coactivator-associated arginine methyltransferase 1


Mass: 38774.160 Da / Num. of mol.: 2 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Carm1, Prmt4 / Production host: unidentified baculovirus / Strain (production host): SF9
References: UniProt: Q4AE70, EC: 2.1.1.125, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 19% PEG 3350, 0.15M sodium malate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→29.49 Å / Num. all: 30000 / Num. obs: 28039 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 20.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2791 / Rsym value: 0.177 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.845 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.432 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26511 1511 5.1 %RANDOM
Rwork0.20539 ---
all0.20835 28325 --
obs0.20835 28039 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 0 57 5233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225306
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9457192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94324.065246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08215896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8531524
X-RAY DIFFRACTIONr_chiral_restr0.0950.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024022
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22252
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23590
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8091.53316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38225216
X-RAY DIFFRACTIONr_scbond_it1.89732270
X-RAY DIFFRACTIONr_scangle_it3.0464.51976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 101 -
Rwork0.232 1959 -
obs--95.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55960.3571-0.06121.45520.25380.90290.0706-0.13590.00060.0834-0.0478-0.0548-0.17890.1162-0.0228-0.0185-0.04580.0183-0.0798-0.0106-0.079518.334-22.743-29.956
20.65610.18640.39360.50340.35881.75430.0767-0.13220.00340.097-0.03210.0212-0.2666-0.0062-0.04460.01880.00560.0363-0.07560.0094-0.0636-16.395-26.945-24.712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA155 - 47816 - 339
2X-RAY DIFFRACTION2BB155 - 47816 - 339

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