[English] 日本語
Yorodumi
- PDB-7pu8: CARM1 in complex with EML980 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pu8
TitleCARM1 in complex with EML980
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSCRIPTION / PROTEIN ARGININE N-METHYLTRANSFERASE / PRMT4 / CARM1 / INHIBITOR
Function / homology
Function and homology information


regulation of growth plate cartilage chondrocyte proliferation / endochondral bone morphogenesis / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway ...regulation of growth plate cartilage chondrocyte proliferation / endochondral bone morphogenesis / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / protein methyltransferase activity / 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 H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / histone H2AQ104 methyltransferase activity / histone methyltransferase activity / nuclear replication fork / positive regulation of fat cell differentiation / nuclear receptor-mediated steroid hormone signaling pathway / protein localization to chromatin / estrogen receptor signaling pathway / : / RNA polymerase II transcription regulator complex / methylation / transcription coactivator activity / cell population proliferation / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol
Similarity search - Function
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 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 ...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 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-4R7 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMarechal, N. / Cura, V. / Troffer-Charlier, N. / Bonnefond, L. / Cavarelli, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction- ...Title: Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach.
Authors: Iannelli, G. / Milite, C. / Marechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / Feoli, A. / Rescigno, D. / Wang, Y. / Cipriano, A. / Viviano, M. / Bedford, M.T. / Cavarelli, J. ...Authors: Iannelli, G. / Milite, C. / Marechal, N. / Cura, V. / Bonnefond, L. / Troffer-Charlier, N. / Feoli, A. / Rescigno, D. / Wang, Y. / Cipriano, A. / Viviano, M. / Bedford, M.T. / Cavarelli, J. / Castellano, S. / Sbardella, G.
History
DepositionSep 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,19712
Polymers163,4024
Non-polymers2,7958
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-41 kcal/mol
Surface area50050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.207, 98.812, 208.401
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: 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 aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9WVG6, type I protein arginine methyltransferase
#2: Chemical
ChemComp-4R7 / methyl 6-[4-[[N-[2-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate


Mass: 636.659 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H36N10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG 2000, 0.1M Sodium Chloride, 0.1M Tris HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→48.07 Å / Num. obs: 80189 / % possible obs: 98.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 46.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.028 / Rrim(I) all: 0.104 / Net I/σ(I): 14.4
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.599 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3738 / CC1/2: 0.543 / Rpim(I) all: 0.492 / Rrim(I) all: 1.678 / % possible all: 81.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.19→48.07 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 3980 4.97 %
Rwork0.1941 76115 -
obs0.1958 80095 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.89 Å2 / Biso mean: 58.2476 Å2 / Biso min: 27.82 Å2
Refinement stepCycle: final / Resolution: 2.19→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11000 0 368 283 11651
Biso mean--64.03 49.52 -
Num. residues----1371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.210.39881160.35441971208772
2.21-2.240.34841520.30952652280499
2.24-2.270.29751410.30482713285499
2.27-2.30.32681420.28512718286099
2.3-2.330.30031410.268427092850100
2.33-2.370.33511140.27042710282499
2.37-2.410.31051330.27132720285399
2.41-2.440.28021540.25626952849100
2.44-2.490.34381490.3032716286599
2.49-2.530.34091210.27392734285599
2.53-2.580.29711600.264827062866100
2.58-2.630.30471330.23772712284599
2.63-2.690.25721530.22552716286999
2.69-2.750.26731290.21342751288099
2.75-2.820.24371380.218127332871100
2.82-2.90.26631460.213327412887100
2.9-2.980.25431190.229527232842100
2.98-3.080.27741560.235827292885100
3.08-3.190.28011520.23327492901100
3.19-3.320.25341410.21827342875100
3.32-3.470.22621310.194327842915100
3.47-3.650.23121380.181227702908100
3.65-3.880.19731540.171727512905100
3.88-4.180.20241590.157427802939100
4.18-4.60.14881470.134527812928100
4.6-5.260.18271320.132128302962100
5.27-6.630.17951570.170228422999100
6.63-48.070.2021720.17022945311799
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)
11.6398-0.9510.14371.0968-0.19992.3257-0.0082-0.27940.34170.156-0.0473-0.0433-0.31890.14940.04790.4331-0.11640.03810.4024-0.08730.438755.226940.3638134.3741
21.97080.16730.9218-0.05070.15521.1620.1935-0.0837-0.11570.0996-0.09920.04820.0680.0748-0.09630.3309-0.02580.03530.2675-0.00970.424446.3112.038118.6792
31.39220.17450.24973.28661.15831.3616-0.0789-0.0370.01340.054-0.0016-0.2511-0.14160.15990.10130.3113-0.07520.03030.368-0.00160.373761.668620.727123.1426
40.8155-0.1328-0.39472.141-0.3791.9304-0.0069-0.069-0.0447-0.162-0.0155-0.1720.01820.30410.00230.2503-0.07380.02240.33-0.02150.338362.286918.7712121.6021
52.7683-0.32860.33434.09890.41151.27820.0828-0.0499-0.14730.2131-0.19430.41330.236-0.39060.10350.3277-0.07250.0390.33370.01380.340253.288617.3746115.79
61.7838-0.24670.00271.26491.11373.16930.14920.07080.1971-0.1636-0.00570.0444-0.3562-0.2136-0.13830.37190.06320.04360.27940.06320.396319.932519.7608115.2334
72.64071.55630.14811.00580.5931.0060.3547-0.59580.1130.3167-0.25550.106-0.02120.0455-0.09550.49420.0210.05320.43610.00490.388933.051727.4481144.7781
84.01630.06941.64531.55110.71284.9240.1613-0.4867-0.16520.27760.02770.22480.1596-0.5969-0.2120.40480.01230.0960.39080.01440.417417.264721.8441138.4829
91.54680.18480.54851.43871.53533.52150.1635-0.33390.05310.2342-0.08350.09540.0241-0.5199-0.07790.34440.00450.06890.44540.08420.371917.170422.4921140.8931
102.16650.0114-0.84291.60460.63296.39210.2753-0.3381-0.0784-0.1891-0.032-0.2551-0.46970.4737-0.29620.46270.00380.06070.38960.00080.452224.639630.4334142.6316
112.5450.16550.07091.2009-0.27132.44760.08860.24670.3136-0.0056-0.02480.0144-0.5084-0.2045-0.0760.48610.07530.0820.40480.01360.331122.34741.4919178.3904
121.5713-0.52150.62960.0786-0.33641.27380.04590.0486-0.1510.0663-0.03510.1265-0.0205-0.19940.00070.371-0.02140.01720.3202-0.02910.377729.674912.5705194.206
132.1785-0.4829-0.4393.9296-0.77071.94370.0920.0966-0.1318-0.089-0.12430.3211-0.2726-0.30740.02820.39450.05250.0350.506-0.04210.317314.868322.23189.5372
141.0036-0.6914-0.16372.4245-0.0822.0276-0.03510.0737-0.15060.26260.03020.3729-0.0169-0.48760.01310.34840.01690.08230.4833-0.04620.407314.034120.3684191.0557
153.45181.3144-0.36314.6792-1.32041.6648-0.02730.171-0.23720.1178-0.1032-0.05590.2048-0.19660.14650.44160.04020.03340.4083-0.04990.372922.855318.387197.0863
161.67780.2135-0.06472.0038-0.62343.06040.2028-0.21390.18280.238-0.0904-0.1153-0.32770.3465-0.10610.3593-0.09690.03590.3615-0.0740.331556.645618.2103197.5387
172.3435-1.31290.00120.4906-0.37190.22830.34580.6288-0.0146-0.2048-0.2663-0.02750.08170.0566-0.08740.5179-0.05340.03990.611-0.05920.472143.777127.1818167.9833
183.342-0.33320.83621.1245-0.17993.92860.1580.4593-0.0501-0.1259-0.0246-0.10070.04620.4905-0.1520.4366-0.00980.10460.4821-0.01250.461858.956520.5348174.2865
191.2242-0.32911.10251.3547-1.22132.57430.17340.3339-0.0167-0.2224-0.1713-0.02890.03110.4908-0.00610.3783-0.03730.06930.5306-0.10560.393959.22421.158171.8524
201.01280.19220.59881.6156-0.36194.53150.2670.22010.05710.1155-0.15430.4291-0.4641-0.2398-0.1230.4543-0.01550.06550.4504-0.04220.499852.763630.251169.9427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 136:282)A136 - 282
2X-RAY DIFFRACTION2(chain A and resid 283:336)A283 - 336
3X-RAY DIFFRACTION3(chain A and resid 337:365)A337 - 365
4X-RAY DIFFRACTION4(chain A and resid 366:445)A366 - 445
5X-RAY DIFFRACTION5(chain A and resid 446:478)A446 - 478
6X-RAY DIFFRACTION6(chain B and resid 135:282)B135 - 282
7X-RAY DIFFRACTION7(chain B and resid 283:336)B283 - 336
8X-RAY DIFFRACTION8(chain B and resid 337:365)B337 - 365
9X-RAY DIFFRACTION9(chain B and resid 366:445)B366 - 445
10X-RAY DIFFRACTION10(chain B and resid 446:477)B446 - 477
11X-RAY DIFFRACTION11(chain C and resid 136:282)C136 - 282
12X-RAY DIFFRACTION12(chain C and resid 283:336)C283 - 336
13X-RAY DIFFRACTION13(chain C and resid 337:365)C337 - 365
14X-RAY DIFFRACTION14(chain C and resid 366:445)C366 - 445
15X-RAY DIFFRACTION15(chain C and resid 446:478)C446 - 478
16X-RAY DIFFRACTION16(chain D and resid 136:282)D136 - 282
17X-RAY DIFFRACTION17(chain D and resid 283:336)D283 - 336
18X-RAY DIFFRACTION18(chain D and resid 337:365)D337 - 365
19X-RAY DIFFRACTION19(chain D and resid 366:445)D366 - 445
20X-RAY DIFFRACTION20(chain D and resid 446:476)D446 - 476

+
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