[English] 日本語
Yorodumi
- PDB-5lgs: Crystal structure of mouse CARM1 in complex with ligand P2C3u -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lgs
TitleCrystal structure of mouse CARM1 in complex with ligand P2C3u
Components
  • Histone-arginine methyltransferase CARM1
  • Polyadenylate-binding protein 1
KeywordsTRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE / CATALYTIC DOMAIN / CHROMATIN REGULATOR / MRNA PROCESSING / MRNA SPLICING / NUCLEUS / S-ADENOSYL-L-METHIONINE / TRANSCRIPTION / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


histone H3R26 methyltransferase activity / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / endochondral bone morphogenesis / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity ...histone H3R26 methyltransferase activity / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / endochondral bone morphogenesis / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / negative regulation of dendrite development / type I protein arginine methyltransferase / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / protein methyltransferase activity / Estrogen-dependent gene expression / 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 / intracellular estrogen receptor signaling pathway / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / intracellular steroid hormone receptor signaling pathway / response to cAMP / protein localization to chromatin / catalytic step 2 spliceosome / nuclear receptor coactivator activity / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / lysine-acetylated histone binding / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / RNA polymerase II transcription regulator complex / lamellipodium / methylation / DNA-binding transcription factor binding / cell population proliferation / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / 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
1,2-DIMETHOXYETHANE / DI(HYDROXYETHYL)ETHER / Chem-QVR / Polyadenylate-binding protein 1 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMarechal, N. / Troffer-Charlier, N. / Cura, V. / Bonnefond, L. / Cavarelli, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1.
Authors: van Haren, M.J. / Marechal, N. / Troffer-Charlier, N. / Cianciulli, A. / Sbardella, G. / Cavarelli, J. / Martin, N.I.
History
DepositionJul 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
E: Polyadenylate-binding protein 1
F: Polyadenylate-binding protein 1
G: Polyadenylate-binding protein 1
H: Polyadenylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,12421
Polymers167,1628
Non-polymers1,96213
Water10,521584
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-81 kcal/mol
Surface area51000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.986, 98.596, 208.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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


Mass: 40850.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Carm1, Prmt4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Protein/peptide
Polyadenylate-binding protein 1 / Poly(A)-binding protein 1


Mass: 940.075 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: PABP1(456-466) PAAPRPPFSTM / Source: (synth.) Homo sapiens (human) / References: UniProt: P11940

-
Non-polymers , 7 types, 597 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DXE / 1,2-DIMETHOXYETHANE / Dimethoxyethane


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-QVR / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol


Mass: 277.279 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15N5O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-HCl pH 8.5 100 mM PEG 3350 20 % A.S. 200 mM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→47.971 Å / Num. obs: 90877 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.753 / Mean I/σ(I) obs: 0.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.1→47.971 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 4503 4.96 %Random selection
Rwork0.1863 ---
obs0.1877 90760 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11266 0 135 584 11985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211747
X-RAY DIFFRACTIONf_angle_d0.51615913
X-RAY DIFFRACTIONf_dihedral_angle_d14.4436988
X-RAY DIFFRACTIONf_chiral_restr0.0431729
X-RAY DIFFRACTIONf_plane_restr0.0032089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.3771330.33862818X-RAY DIFFRACTION100
2.1239-2.14890.35091530.32272861X-RAY DIFFRACTION100
2.1489-2.17510.31111580.31862826X-RAY DIFFRACTION100
2.1751-2.20260.34441420.31042843X-RAY DIFFRACTION100
2.2026-2.23160.36421730.3092807X-RAY DIFFRACTION100
2.2316-2.26220.31991440.28962853X-RAY DIFFRACTION100
2.2622-2.29450.28281550.2762869X-RAY DIFFRACTION100
2.2945-2.32870.25331400.25552836X-RAY DIFFRACTION100
2.3287-2.36510.31781230.24842861X-RAY DIFFRACTION100
2.3651-2.40390.26591490.24172847X-RAY DIFFRACTION100
2.4039-2.44530.241610.22652833X-RAY DIFFRACTION100
2.4453-2.48980.2471510.22532868X-RAY DIFFRACTION100
2.4898-2.53770.25591270.21432870X-RAY DIFFRACTION100
2.5377-2.58950.24731650.2152847X-RAY DIFFRACTION100
2.5895-2.64580.23311430.2112849X-RAY DIFFRACTION100
2.6458-2.70730.23491570.20582823X-RAY DIFFRACTION100
2.7073-2.7750.26821300.2152905X-RAY DIFFRACTION100
2.775-2.850.24841560.20622859X-RAY DIFFRACTION100
2.85-2.93390.22811430.19312870X-RAY DIFFRACTION100
2.9339-3.02860.21511480.19432868X-RAY DIFFRACTION100
3.0286-3.13680.20161670.19842851X-RAY DIFFRACTION100
3.1368-3.26240.21751380.18842932X-RAY DIFFRACTION100
3.2624-3.41080.221500.1852881X-RAY DIFFRACTION100
3.4108-3.59060.20891330.16982882X-RAY DIFFRACTION100
3.5906-3.81540.18981550.152886X-RAY DIFFRACTION100
3.8154-4.10990.16061730.1372900X-RAY DIFFRACTION100
4.1099-4.52320.15191550.12812908X-RAY DIFFRACTION100
4.5232-5.17710.16051360.12142967X-RAY DIFFRACTION100
5.1771-6.51990.18561680.16142965X-RAY DIFFRACTION100
6.5199-47.98370.19491770.17663072X-RAY DIFFRACTION99
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)
11.40650.0896-0.22790.8177-0.02960.96110.0051-0.16640.16680.0824-0.03620.016-0.04950.0900.3192-0.04850.02880.206-0.07660.317255.100640.0472134.3161
20.97070.38720.3154-0.44670.10550.40570.0047-0.0168-0.01980.00990.01710.0451-0.00690.062700.20660.0053-0.00720.1432-0.01680.352248.001411.9541119.8569
30.3004-0.1235-0.17421.38760.07111.2527-0.0377-0.0348-0.059-0.10520.0044-0.0510.00010.0854-00.206-0.03890.04410.1917-0.02130.316760.395519.3536119.847
41.066-0.258-0.1380.95030.28751.36430.10410.0265-0.00680.0060.0076-0.0042-0.1816-0.15240.0010.25270.07460.02740.19430.03890.318619.008319.8713115.5947
50.41650.30830.2177-0.1118-0.01880.05650.1788-0.13210.0020.1298-0.02570.02410.00210.019200.4328-0.02620.06050.4458-0.03060.372938.31528.6263149.103
60.49510.11170.12060.67460.64190.55310.1146-0.23930.21250.0029-0.1169-0.06730.0943-0.19090.00020.33640.02990.06970.39030.0470.357117.157821.5234138.592
70.7135-0.0809-0.2408-0.10920.37890.7290.0738-0.2641-0.05560.07650.02230.0720.0146-0.150300.32950.02520.04890.35050.04750.340116.999222.3698140.7299
80.548-0.08690.57490.14030.01680.44220.0618-0.1693-0.19690.021-0.0039-0.1863-0.12050.143200.40550.00940.070.37260.0380.434624.558329.7736142.4957
91.05540.0505-0.41580.3419-0.56950.8046-0.02130.07360.10180.03480.10340.0268-0.2851-0.21190.00010.56980.11070.04520.5541-0.00050.336323.221441.7341176.0899
100.1345-0.10940.27610.1687-0.09570.29740.1227-0.0071-0.14110.0131-0.07470.0539-0.0933-0.1770.03480.3810.05670.04860.5197-0.0150.308626.067421.0556191.9072
110.3482-0.2046-0.73590.8114-0.03670.6779-0.07170.0331-0.05920.04670.01480.0422-0.0336-0.2222-0.00090.37750.06090.07430.5753-0.0270.330316.171520.1191191.9946
121.03290.5104-0.35211.1326-0.19461.22650.1861-0.1468-0.03880.1135-0.1335-0.0577-0.20670.231100.4266-0.12480.02080.5669-0.04890.325757.415918.141196.8741
130.3378-0.53480.26880.06110.02780.33660.16430.1022-0.04470.0914-0.09410.0322-0.05290.0276-00.48740.00160.06740.5712-0.02070.356939.920227.4807164.7858
140.10050.05970.14350.1231-0.16010.3006-0.0250.3304-0.07940.0831-0.0450.0807-0.08870.5074-00.4929-0.01250.02590.6768-0.0390.368563.65423.0724176.1786
150.44330.3417-0.42540.2244-0.42060.35140.13890.1241-0.0652-0.0484-0.1067-0.0389-0.010.2325-00.46550.02880.01740.5787-0.05240.375158.601317.2488171.2267
160.4512-0.23620.42860.4589-0.40260.41050.30670.07520.03060.1559-0.12310.0943-0.2596-0.000700.5494-0.03230.05170.6448-0.03610.403854.658129.1229169.8354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 136:282)
2X-RAY DIFFRACTION2(chain A and resid 283:349)
3X-RAY DIFFRACTION3(chain A and resid 350:478)
4X-RAY DIFFRACTION4(chain B and resid 135:293)
5X-RAY DIFFRACTION5(chain B and resid 294:336)
6X-RAY DIFFRACTION6(chain B and resid 337:365)
7X-RAY DIFFRACTION7(chain B and resid 366:445)
8X-RAY DIFFRACTION8(chain B and resid 446:477)
9X-RAY DIFFRACTION9(chain C and resid 136:257)
10X-RAY DIFFRACTION10(chain C and resid 258:336)
11X-RAY DIFFRACTION11(chain C and resid 337:478)
12X-RAY DIFFRACTION12(chain D and resid 136:293)
13X-RAY DIFFRACTION13(chain D and resid 294:344)
14X-RAY DIFFRACTION14(chain D and resid 345:372)
15X-RAY DIFFRACTION15(chain D and resid 373:430)
16X-RAY DIFFRACTION16(chain D and resid 431:477)

+
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