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- PDB-5dx1: Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455) -

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Basic information

Entry
Database: PDB / ID: 5dx1
TitleCrystal structure of CARM1, sinefungin, and PABP1 peptide (R455)
Components
  • Histone-arginine methyltransferase CARM1
  • PABP1 peptide
KeywordsTRANSFERASE / protein-substrate ternary complex
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / protein methyltransferase activity / Deadenylation of mRNA / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / positive regulation of cytoplasmic translation / protein-arginine N-methyltransferase activity / mRNA stabilization / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of epithelial cell apoptotic process / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / : / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / nuclear replication fork / cell leading edge / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of fat cell differentiation / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / response to cAMP / catalytic step 2 spliceosome / 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) / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cytoplasmic ribonucleoprotein granule / PPARA activates gene expression / Cytoprotection by HMOX1 / mRNA splicing, via spliceosome / RMTs methylate histone arginines / beta-catenin binding / Regulation of expression of SLITs and ROBOs / Transcriptional regulation of white adipocyte differentiation / cytoplasmic stress granule / Circadian Clock / lamellipodium / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / ribonucleoprotein complex / focal adhesion / mRNA binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) 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 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / 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 / RNA recognition motif domain, eukaryote / RNA recognition motif / 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: 1.93 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

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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
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
F: PABP1 peptide
G: PABP1 peptide
H: PABP1 peptide
I: PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,08416
Polymers166,1908
Non-polymers1,8948
Water8,827490
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
F: PABP1 peptide
G: PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1349
Polymers83,0954
Non-polymers1,0395
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-36 kcal/mol
Surface area26950 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
H: PABP1 peptide
I: PABP1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9507
Polymers83,0954
Non-polymers8553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-37 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.002, 98.322, 208.152
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
PABP1 peptide


Mass: 1924.296 Da / Num. of mol.: 4 / Fragment: UNP residues 449-466
Mutation: Nterminal biotin and aminohexanoic acid, methylated R460
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.32 %
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: Aug 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 110682 / % possible obs: 99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.9
Reflection shellResolution: 1.93→2.08 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3.2 / % possible all: 97

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.93→45.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.137 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5771 5 %RANDOM
Rwork0.1958 ---
obs0.1979 109335 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.81 Å2 / Biso mean: 30.504 Å2 / Biso min: 14.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2---0.28 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.93→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11313 0 132 490 11935
Biso mean--28.28 34.93 -
Num. residues----1414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912074
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211357
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.95816417
X-RAY DIFFRACTIONr_angle_other_deg0.792326123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0851488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90423.737562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.825152001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8851567
X-RAY DIFFRACTIONr_chiral_restr0.0810.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022983
X-RAY DIFFRACTIONr_mcbond_it1.6612.8795823
X-RAY DIFFRACTIONr_mcbond_other1.6612.8785822
X-RAY DIFFRACTIONr_mcangle_it2.5514.3037309
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 407 -
Rwork0.325 7904 -
all-8311 -
obs--98.36 %

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