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- PDB-5dxa: Crystal structure of CARM1, sinefungin, and methylated PABP1 pept... -

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Basic information

Entry
Database: PDB / ID: 5dxa
TitleCrystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R460)
Components
  • Histone-arginine methyltransferase CARM1
  • methylated PABP1 peptide
KeywordsTRANSFERASE / protein-substrate ternary complex
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation activator activity / negative regulation of dendrite development / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / histone arginine N-methyltransferase activity ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation activator activity / negative regulation of dendrite development / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / histone arginine N-methyltransferase activity / protein methyltransferase activity / Deadenylation of mRNA / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H4R3 methyltransferase activity / poly(A) binding / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / regulatory ncRNA-mediated gene silencing / mRNA stabilization / positive regulation of epithelial cell apoptotic process / histone H2AQ104 methyltransferase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / histone methyltransferase activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / positive regulation of transcription by RNA polymerase I / cell leading edge / nuclear replication fork / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of fat cell differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / response to cAMP / : / Regulation of lipid metabolism by PPARalpha / catalytic step 2 spliceosome / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mRNA 3'-UTR binding / : / AUF1 (hnRNP D0) binds and destabilizes mRNA / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / mRNA splicing, via spliceosome / Transcriptional regulation of white adipocyte differentiation / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / : / lamellipodium / DNA-binding transcription factor binding / methylation / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / ribonucleoprotein complex / focal adhesion / mRNA binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal ...: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / RNA recognition motif domain, eukaryote / RNA recognition motif / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Distorted Sandwich / PH-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Polyadenylate-binding protein 1 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsBoriack-Sjodin, P.A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates.
Authors: Boriack-Sjodin, P.A. / Jin, L. / Jacques, S.L. / Drew, A. / Sneeringer, C. / Scott, M.P. / Moyer, M.P. / Ribich, S. / Moradei, O. / Copeland, R.A.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

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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
F: methylated PABP1 peptide
G: methylated PABP1 peptide
I: methylated PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,14814
Polymers164,3477
Non-polymers1,8027
Water9,098505
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
F: methylated PABP1 peptide
G: methylated PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0968
Polymers83,1494
Non-polymers9474
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-41 kcal/mol
Surface area26320 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
I: methylated PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0526
Polymers81,1983
Non-polymers8553
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-32 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.179, 98.693, 207.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 39623.121 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 134-479)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFastBac / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86X55, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Protein/peptide methylated PABP1 peptide / Poly(A)-binding protein 1


Mass: 1951.341 Da / Num. of mol.: 3 / Fragment: UNP residues 449-466
Mutation: Nterminal biotin and aminohexanoic acid, methylated R460, asymmetrically dimethylated R455
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P11940
#3: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe N-terminal of PABP1 peptide is modified with biotin and aminohexanoic acid.

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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: 49.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.07→48.1 Å / Num. obs: 94364 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.7
Reflection shellResolution: 2.07→2.19 Å / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.07→44.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.514 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4730 5 %RANDOM
Rwork0.1981 ---
obs0.2005 89629 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.25 Å2 / Biso mean: 28.571 Å2 / Biso min: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.14 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.07→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11178 0 126 505 11809
Biso mean--25.22 31.26 -
Num. residues----1393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911931
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211174
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.95616224
X-RAY DIFFRACTIONr_angle_other_deg0.782325712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15451464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54123.864559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.628151975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6051560
X-RAY DIFFRACTIONr_chiral_restr0.0770.21769
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022959
X-RAY DIFFRACTIONr_mcbond_it1.4592.7465733
X-RAY DIFFRACTIONr_mcbond_other1.4592.7465732
X-RAY DIFFRACTIONr_mcangle_it2.2674.1097196
LS refinement shellResolution: 2.065→2.119 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 349 -
Rwork0.309 6430 -
all-6779 -
obs--97.67 %

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