[English] 日本語
Yorodumi
- PDB-5dxa: Crystal structure of CARM1, sinefungin, and methylated PABP1 pept... -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / translation activator activity / histone H3R17 methyltransferase 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 / : / translation activator activity / histone H3R17 methyltransferase 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 / protein-arginine N-methyltransferase activity / positive regulation of cytoplasmic translation / 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 / : / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more