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- PDB-7os4: Crystal structure of mouse CARM1 in complex with histone H3_13-31 K18 -

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Basic information

Entry
Database: PDB / ID: 7os4
TitleCrystal structure of mouse CARM1 in complex with histone H3_13-31 K18
Components
  • Histone H3.1Histone H3
  • Histone-arginine methyltransferase CARM1
KeywordsTRANSCRIPTION / protein arginine N-methyltransferase / PRMT / CARM1 / transition state mimics
Function / homology
Function and homology information


Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / histone H3R26 methyltransferase activity / PRC2 methylates histones and DNA / HATs acetylate histones / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / PKMTs methylate histone lysines ...Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / histone H3R26 methyltransferase activity / PRC2 methylates histones and DNA / HATs acetylate histones / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / PKMTs methylate histone lysines / histone H3R2 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / protein methyltransferase activity / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / nuclear replication fork / positive regulation of fat cell differentiation / intracellular estrogen receptor signaling pathway / intracellular steroid hormone receptor signaling pathway / response to cAMP / protein localization to chromatin / nuclear receptor coactivator activity / lysine-acetylated histone binding / structural constituent of chromatin / RNA polymerase II transcription regulator complex / nucleosome / chromatin organization / methylation / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / protein heterodimerization activity / 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 / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-QVR / Histone H3.1 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsMarechal, N. / Cura, V. / Troffer-Charlier, N. / Bonnefond, L. / Cavarelli, J.
CitationJournal: Chembiochem / Year: 2021
Title: Structural Studies Provide New Insights into the Role of Lysine Acetylation on Substrate Recognition by CARM1 and Inform the Design of Potent Peptidomimetic Inhibitors.
Authors: Zhang, Y. / Marechal, N. / van Haren, M.J. / Troffer-Charlier, N. / Cura, V. / Cavarelli, J. / Martin, N.I.
History
DepositionJun 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Histone H3.1
F: Histone H3.1
G: Histone H3.1
H: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,98112
Polymers175,8728
Non-polymers1,1094
Water1,08160
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
E: Histone H3.1
F: Histone H3.1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
E: Histone H3.1
F: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,98112
Polymers175,8728
Non-polymers1,1094
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area22070 Å2
ΔGint-108 kcal/mol
Surface area48900 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
G: Histone H3.1
H: Histone H3.1
hetero molecules

C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
G: Histone H3.1
H: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,98112
Polymers175,8728
Non-polymers1,1094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area22190 Å2
ΔGint-98 kcal/mol
Surface area48910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.374, 98.606, 206.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-505-

HOH

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Components

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


Mass: 41985.637 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: Protein/peptide
Histone H3.1 / Histone H3


Mass: 1982.376 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The is a chemical modification. There is a fusion between the chemical compound referred as QVR and an arginine (R).
Source: (synth.) Mus musculus (house mouse) / References: UniProt: P68433
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.2M Sodium malonate 0.1M MES pH 5.5 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→45.76 Å / Num. obs: 49843 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 63.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Net I/σ(I): 8.6
Reflection shellResolution: 2.54→2.62 Å / Redundancy: 5.5 % / Rmerge(I) obs: 2.284 / Num. unique obs: 4042 / CC1/2: 0.475 / Rpim(I) all: 0.996 / Rrim(I) all: 2.501 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.54→45.76 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2460 4.95 %
Rwork0.2079 47227 -
obs0.2103 49687 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.14 Å2 / Biso mean: 65.2003 Å2 / Biso min: 33.13 Å2
Refinement stepCycle: final / Resolution: 2.54→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11624 0 0 60 11684
Biso mean---57.91 -
Num. residues----1449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.590.4251150.39552181229682
2.59-2.640.3981260.35812506263295
2.64-2.70.3591330.32722551268497
2.7-2.760.34811260.30352654278099
2.76-2.830.35881370.288426532790100
2.83-2.910.31331330.285426352768100
2.91-2.990.31331360.27862656279299
2.99-3.090.30971480.25082653280199
3.09-3.20.30661430.238526302773100
3.2-3.330.28971320.234426762808100
3.33-3.480.28511170.22592645276298
3.48-3.670.27251190.19862439255891
3.67-3.890.23341600.18372656281699
3.89-4.20.22151440.169226582802100
4.2-4.620.20191440.159727062850100
4.62-5.280.22431310.156427302861100
5.28-6.650.24471530.201327452898100
6.65-45.760.19921630.16982853301698
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)
12.0758-0.3803-0.54651.0810.41782.23530.0871-0.02490.3560.0933-0.0756-0.0636-0.44810.159-0.0210.5286-0.17470.00650.43850.01630.566654.61939.881133.414
22.14470.3240.81940.16070.51231.16490.06480.1468-0.18090.02620.0617-0.1225-0.1140.3512-0.13350.2753-0.02050.01580.50510.06920.442245.84211.887117.254
30.93950.0727-0.20871.9090.33390.77670.0372-0.1439-0.0801-0.1001-0.1052-0.2679-0.25510.40310.07670.3577-0.06280.0490.65010.11140.508961.20320.388121.882
40.51290.5394-0.23111.59510.19062.0646-0.01120.26120.0479-0.0578-0.0323-0.3485-0.00050.68590.0710.2886-0.02640.02590.63870.06890.556661.56118.584120.415
50.68260.23040.33932.7432-0.29831.4960.15560.1572-0.2206-0.2228-0.03850.3885-0.11830.0481-0.05790.29270.03870.05930.623-0.01410.44652.9417.287114.138
62.3723-1.40580.39345.054-1.08162.5412-0.230.6864-0.2950.6145-0.227-0.0658-0.58840.910.44290.6235-0.07250.01820.8593-0.05550.62259.937-2.17132.244
71.30350.2611-0.47842.06720.12852.48940.16450.23220.1189-0.079-0.03380.1714-0.3521-0.1731-0.10190.35160.17570.0550.58820.07350.430819.56719.362114.056
81.25030.555-0.59370.9796-0.01891.04010.2705-0.40930.12310.316-0.29130.1778-0.3908-0.2305-0.00470.58260.05520.11190.4725-0.01050.417932.75526.646143.549
92.4227-0.96720.59361.86130.96112.48390.1648-0.23970.02360.0907-0.04390.2707-0.1427-0.2588-0.07950.4031-0.05030.11870.66430.02290.553917.14221.131137.235
101.5441-0.39970.45040.52890.78621.99870.0267-0.26770.12620.18440.00940.1169-0.1471-0.6199-0.06570.45080.02450.09040.6010.05030.430916.92821.697139.815
111.58840.01520.14341.03081.09362.70150.2231-0.09280.1917-0.19740.4157-0.3543-0.33920.1418-0.53250.616-0.01190.15270.4844-0.00320.607424.9628.953141.126
121.6833-0.1167-0.96311.9459-0.29491.34760.1167-0.00790.4120.2166-0.07920.0202-0.3495-0.2566-0.04970.78010.0730.11180.5014-0.02520.531122.3840.863176.536
131.5223-0.15910.4270.7601-0.41031.47490.1302-0.0999-0.15020.2656-0.01390.1548-0.3274-0.2679-0.14380.5852-0.07020.08380.4579-0.07820.422429.38912.403192.858
142.0756-0.3186-0.26892.69520.12640.32070.14390.2075-0.15940.1453-0.15570.028-0.1821-0.40490.02950.6203-0.05340.07310.6137-0.05520.484914.53522.018188.019
150.8664-0.5334-0.35612.11940.50891.27120.1453-0.04340.04220.3222-0.15490.23070.0301-0.62220.05710.5947-0.0580.10510.5847-0.09110.502713.95220.162189.543
160.4781-0.6370.43361.7746-0.82541.31660.0775-0.1087-0.08610.3253-0.13980.1937-0.19990.22980.02990.7071-0.04530.18640.6919-0.05220.579822.518.349195.96
171.58060.8106-0.13762.41820.0061.2124-0.16250.4867-0.14930.11920.1437-0.3668-0.2832-0.83540.03541.0862-0.13580.13510.86240.04880.701714.445-0.668177.911
182.1285-0.0373-0.38571.3175-0.32142.09820.2409-0.3080.07110.31-0.2126-0.0972-0.40810.249-0.01730.6474-0.25390.00470.5311-0.0620.440756.22118.091196.096
191.5511-0.3786-0.32980.92530.40740.21270.28640.2690.2033-0.1591-0.3028-0.0234-0.26260.10890.03270.7154-0.10610.11380.46170.00990.434243.51926.339166.521
202.2926-0.09331.49350.773-0.56511.97480.160.312-0.02810.1597-0.0157-0.0714-0.01920.3549-0.0150.6084-0.0030.13040.5172-0.00370.530758.56119.837172.793
211.40260.3490.85091.3676-1.54932.41190.04150.43540.0728-0.1129-0.0652-0.1372-0.04310.5501-0.00310.5496-0.04920.05880.5603-0.04920.448558.7620.322170.481
221.8868-0.957-0.00941.1692-1.45173.09450.3870.21430.217-0.0030.1720.2506-0.4462-0.3214-0.64760.8247-0.09420.11580.56550.03690.653351.59927.942168.756
233.32390.47290.18325.4399-0.83322.5868-0.3042-0.57420.83470.12520.0328-0.2338-0.0146-0.0565-0.00710.5324-0.0402-0.02480.69-0.01550.657447.27226.878131.108
244.1479-2.07852.09042.6419-2.43064.97660.08480.4943-0.0550.4119-0.07630.5867-0.13330.9506-0.31570.64260.10370.09160.82350.09720.694229.96818.77124.9
252.0603-0.62330.07062.2693-0.61551.4242-0.04050.04220.6328-0.5801-0.5640.1195-0.29110.43850.66660.9468-0.08990.0710.6799-0.11420.550128.9127.466179.006
261.97080.88130.4082.95681.30422.23430.1193-0.02730.11541.1345-0.45520.54860.5456-0.52130.27930.96340.03370.03420.8713-0.13630.675945.77318.386185.302
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 446:477 )A446 - 477
6X-RAY DIFFRACTION6( CHAIN A AND RESID 478:495 )A478 - 495
7X-RAY DIFFRACTION7( CHAIN B AND RESID 136:282 )B136 - 282
8X-RAY DIFFRACTION8( CHAIN B AND RESID 283:336 )B283 - 336
9X-RAY DIFFRACTION9( CHAIN B AND RESID 337:365 )B337 - 365
10X-RAY DIFFRACTION10( CHAIN B AND RESID 366:445 )B366 - 445
11X-RAY DIFFRACTION11( CHAIN B AND RESID 446:478 )B446 - 478
12X-RAY DIFFRACTION12( CHAIN C AND RESID 137:282 )C137 - 282
13X-RAY DIFFRACTION13( CHAIN C AND RESID 283:336 )C283 - 336
14X-RAY DIFFRACTION14( CHAIN C AND RESID 337:365 )C337 - 365
15X-RAY DIFFRACTION15( CHAIN C AND RESID 366:445 )C366 - 445
16X-RAY DIFFRACTION16( CHAIN C AND RESID 446:477 )C446 - 477
17X-RAY DIFFRACTION17( CHAIN C AND RESID 478:495 )C478 - 495
18X-RAY DIFFRACTION18( CHAIN D AND RESID 136:282 )D136 - 282
19X-RAY DIFFRACTION19( CHAIN D AND RESID 283:336 )D283 - 336
20X-RAY DIFFRACTION20( CHAIN D AND RESID 337:365 )D337 - 365
21X-RAY DIFFRACTION21( CHAIN D AND RESID 366:445 )D366 - 445
22X-RAY DIFFRACTION22( CHAIN D AND RESID 446:478 )D446 - 478
23X-RAY DIFFRACTION23( CHAIN E AND RESID 12:22 )E12 - 22
24X-RAY DIFFRACTION24( CHAIN F AND RESID 12:22 )F12 - 22
25X-RAY DIFFRACTION25( CHAIN G AND RESID 12:22 )G12 - 22
26X-RAY DIFFRACTION26( CHAIN H AND RESID 12:22 )H12 - 22

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