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- PDB-2oqb: Crystal structure of the N-terminal domain of coactivator-associa... -

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Basic information

Entry
Database: PDB / ID: 2oqb
TitleCrystal structure of the N-terminal domain of coactivator-associated methyltransferase 1 (CARM1)
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / GENE REGULATION / Protein Arginine methyltransferase / transcriptional regulation / activation domain
Function / homology
Function and homology information


Estrogen-dependent gene expression / RMTs methylate histone arginines / 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 / type I protein arginine methyltransferase ...Estrogen-dependent gene expression / RMTs methylate histone arginines / 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 / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein 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 / nuclear receptor-mediated steroid hormone signaling pathway / response to cAMP / protein localization to chromatin / estrogen receptor signaling pathway / RNA splicing / nuclear receptor coactivator activity / lysine-acetylated histone binding / mRNA processing / RNA polymerase II transcription regulator complex / DNA-binding transcription factor binding / methylation / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / 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) / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.69 Å
AuthorsCavarelli, J.
CitationJournal: 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.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7333
Polymers25,6972
Non-polymers351
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-5 kcal/mol
Surface area11430 Å2
MethodPISA, PQS
2
A: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
hetero molecules

B: Histone-arginine methyltransferase CARM1

B: Histone-arginine methyltransferase CARM1


Theoretical massNumber of molelcules
Total (without water)51,4656
Polymers51,3944
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
crystal symmetry operation6_565x+1/2,-y+3/2,-z+3/41
Buried area5740 Å2
ΔGint-47 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.127, 46.127, 201.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 12848.558 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Carm1, Prmt4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4AE70, EC: 2.1.1.125
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 13%-16% PEG 6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.69→41.92 Å / Num. obs: 25232 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 9.7 / Num. unique all: 2470 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.69→41.92 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.626 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1916 7.6 %RANDOM
Rwork0.205 ---
all0.209 25381 --
obs0.209 25232 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.69→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 1 235 1870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211662
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9372246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3922.59777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6415269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0411516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021266
X-RAY DIFFRACTIONr_nbd_refined0.2060.2649
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.228
X-RAY DIFFRACTIONr_mcbond_it1.0131.51085
X-RAY DIFFRACTIONr_mcangle_it1.62321695
X-RAY DIFFRACTIONr_scbond_it2.3583629
X-RAY DIFFRACTIONr_scangle_it3.5984.5551
LS refinement shellResolution: 1.69→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 154 -
Rwork0.197 1662 -
obs-1816 100 %
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)
10.95730.3734-0.74270.788-0.22361.5527-0.0451-0.01170.0169-0.00840.03940.03280.0163-0.0160.0057-0.03290.0107-0.0033-0.0595-0.0068-0.02445.361823.230970.6708
20.8485-0.12990.01130.89820.48561.9308-0.02330.0144-0.06540.03180.0367-0.03480.12420.0959-0.0134-0.02420.00750.0093-0.03350.0015-0.01830.065224.089793.429
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA24 - 1311 - 108
22BB24 - 1291 - 106

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