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- PDB-3b3j: The 2.55 A crystal structure of the apo catalytic domain of coact... -

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Basic information

Entry
Database: PDB / ID: 3b3j
TitleThe 2.55 A crystal structure of the apo catalytic domain of coactivator-associated arginine methyl transferase I(CARM1:28-507, residues 28-146 and 479-507 not ordered)
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE 4 / apo 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
BENZAMIDINE / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.55 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6767
Polymers53,9551
Non-polymers7216
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.022, 136.022, 125.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 53955.070 Da / Num. of mol.: 1
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: Chemical
ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5% MPD, 100mM sodium citrate, 100 mM NaCl, 100 mM benzamidine chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.55→117.85 Å / Num. all: 21690 / Num. obs: 21499 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 67.4 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 25.9
Reflection shellResolution: 2.55→2.63 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1863 / Rsym value: 0.282 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.55→117.85 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.135 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.313 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26885 1165 5.1 %RANDOM
Rwork0.235 ---
obs0.23674 21499 99.12 %-
all-21690 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.269 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.55→117.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 54 35 2753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9613771
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62224.031129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56915457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0231512
X-RAY DIFFRACTIONr_chiral_restr0.1180.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022147
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21877
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.51710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59622684
X-RAY DIFFRACTIONr_scbond_it2.17631223
X-RAY DIFFRACTIONr_scangle_it3.524.51087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 83 -
Rwork0.281 1578 -
obs--99.34 %
Refinement TLS params.Method: refined / Origin x: 50.53 Å / Origin y: 16.716 Å / Origin z: 57.194 Å
111213212223313233
T0.0196 Å20.0727 Å20.0418 Å2--0.119 Å2-0.0503 Å2---0.0309 Å2
L0.7771 °2-0.0022 °2-0.1703 °2-1.0917 °20.4591 °2--2.5901 °2
S0.0722 Å °0.0747 Å °0.1349 Å °-0.1637 Å °-0.0959 Å °0.2001 Å °-0.0254 Å °-0.0317 Å °0.0237 Å °

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