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- PDB-7qrd: Crystal structure of mouse CARM1 in complex with histone H3_10-25 -

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Basic information

Entry
Database: PDB / ID: 7qrd
TitleCrystal structure of mouse CARM1 in complex with histone H3_10-25
Components
  • Histone-arginine methyltransferase CARM1
  • SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


histone H3R26 methyltransferase activity / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity ...histone H3R26 methyltransferase activity / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Cytoprotection by HMOX1 / protein methyltransferase activity / 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 / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / 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 / RNA polymerase II transcription regulator complex / methylation / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region 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 / 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. / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
MALONATE ION / Chem-QVR / S-ADENOSYL-L-HOMOCYSTEINE / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarechal, N. / Cura, V. / Troffer-Charlier, N. / Bonnefond, L. / Cavarelli, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CARM1 Transition State Mimics
Authors: Marechal, N. / Cura, V. / Troffer-Charlier, N. / Bonnefond, L. / Cavarelli, J.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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
L: SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA
M: SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,08716
Polymers174,3116
Non-polymers1,77610
Water10,359575
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.183, 99.204, 208.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDLM

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


Mass: 42783.402 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 SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA


Mass: 1588.850 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Histone H3.1 / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 5 types, 585 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#6: 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.: 2 / Source method: obtained synthetically / Formula: C12H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20 mM Tris-HCl pH 7.5 50 mM NaCl 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→46.1 Å / Num. obs: 105764 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 43.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.053 / Rrim(I) all: 0.136 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.5 % / Rmerge(I) obs: 3.52 / Num. unique obs: 729 / CC1/2: 0.273 / Rpim(I) all: 1.604 / Rrim(I) all: 3.52 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.20rc2_4400refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2→41.65 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 5252 4.98 %
Rwork0.2224 100207 -
obs0.224 105459 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.43 Å2 / Biso mean: 50.4733 Å2 / Biso min: 22.86 Å2
Refinement stepCycle: final / Resolution: 2→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11519 0 148 575 12242
Biso mean--50.34 44.18 -
Num. residues----1437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.46971580.45843123328193
2.02-2.050.45331900.421332703460100
2.05-2.070.41761940.401633003494100
2.07-2.10.38051560.382733313487100
2.1-2.120.37681600.358933253485100
2.12-2.150.36551660.349333483514100
2.15-2.180.34821870.342532813468100
2.18-2.220.36231800.329733213501100
2.22-2.250.37351870.31873268345599
2.25-2.290.34721780.306833343512100
2.29-2.330.32861620.285732873449100
2.33-2.370.28711570.27133613518100
2.37-2.420.29261690.252933363505100
2.42-2.460.25671940.243832623456100
2.46-2.520.26331620.247533823544100
2.52-2.580.30861740.252233263500100
2.58-2.640.28811660.24683322348899
2.64-2.710.26461810.2333315349699
2.71-2.790.28811600.230533703530100
2.79-2.880.2711740.228833333507100
2.88-2.990.26271570.236733713528100
2.99-3.10.27021990.23383336353599
3.1-3.250.29731650.236933393504100
3.25-3.420.24241780.207934073585100
3.42-3.630.21071510.185633563507100
3.63-3.910.20092010.169833763577100
3.91-4.30.19381920.151433923584100
4.3-4.930.17081610.141334503611100
4.93-6.20.19781830.170534683651100
6.2-41.650.22542100.20333517372797
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)
11.6296-0.4616-0.19171.40430.18291.4796-0.04650.1310.23930.0588-0.0125-0.1311-0.47980.36610.06040.5821-0.21210.04490.42160.04480.349254.758340.1853134.7156
21.59491.16730.27153.73160.34511.04760.0267-0.1087-0.0006-0.096-0.1478-0.3746-0.46950.62590.12760.3703-0.09970.05720.53690.07310.291261.585120.8023123.0156
30.96530.33940.00591.37860.14951.62590.06590.1364-0.0339-0.2724-0.1803-0.2009-0.04970.65280.04580.3115-0.07380.06440.57240.08290.338862.082118.9823121.4392
40.9011-0.38360.61472.00590.61151.0754-0.02340.143-0.2079-0.1786-0.07740.07610.03460.2910.10680.4931-0.07610.120.44680.05790.378453.372517.6251115.0678
52.1819-0.9685-0.414.7991-1.30212.96460.0853-0.1964-0.12940.7089-0.25810.2666-0.78720.69450.25530.5078-0.11310.03050.5991-0.03010.409961.5255-4.0708135.7199
61.4288-0.2104-0.21721.69440.62452.48960.2470.18670.0458-0.2132-0.10360.0761-0.4177-0.5073-0.10910.44360.20480.0320.49960.09670.288819.554819.1727114.7989
70.77980.77280.1230.49960.45690.44930.15650.07840.01050.1267-0.0340.0857-0.427-0.094-0.08020.49760.01120.05740.43490.01680.326332.664826.7043144.523
82.64-0.89210.00581.26880.94582.2120.16470.0232-0.10690.0378-0.15420.1172-0.2353-0.3408-0.03550.4650.08820.11080.5660.02940.334317.123921.0683138.0717
91.19380.0310.24730.9090.82222.64010.0991-0.0510.0883-0.0076-0.07220.0913-0.3842-0.5646-0.02820.33210.10270.06320.46750.07270.294417.094721.6667140.5618
102.82610.5266-0.22121.55190.47745.32630.2578-0.0651-0.0703-0.16840.0198-0.0981-0.76860.0975-0.35260.42580.06850.04480.32550.07480.398124.847928.8875142.2632
111.8487-0.2686-0.15591.1772-0.22922.23030.11780.02110.2721-0.0341-0.01470.0428-0.669-0.2913-0.04180.62380.18220.09990.38970.00650.372322.639640.9504177.9022
121.2487-0.19580.4182-0.04010.01731.33810.2244-0.0016-0.08790.0763-0.14560.158-0.1108-0.3492-0.05330.1875-0.00110.04290.2763-0.01430.295529.714412.5196194.4726
131.2275-0.1499-0.40871.7015-0.15731.49960.09940.04150.02830.1562-0.16120.1966-0.2376-0.50140.01870.29170.11410.07750.4567-0.0530.340214.136320.1887190.9775
141.10640.2569-0.19162.2082-0.2211.60670.08330.0491-0.19230.0064-0.1276-0.0925-0.1641-0.21450.05520.37330.0940.05940.5102-0.02430.337722.687318.4672197.4438
150.5160.0218-0.82253.49321.64912.89280.07560.1051-0.0416-0.587-0.43890.0892-0.849-0.20510.39380.50670.0872-0.07250.71780.0080.537313.6442-2.7926176.7642
161.55140.3239-0.26322.039-0.13042.49620.1843-0.18970.10020.0695-0.1104-0.1157-0.27390.3232-0.05520.2766-0.1480.01320.3312-0.03530.310756.820118.1526197.7624
170.7863-0.6980.20850.8714-0.54171.01580.19040.11420.137-0.1709-0.1148-0.0541-0.2851-0.0459-0.04990.4101-0.00660.08040.3651-0.0260.287443.999326.3847168.0112
182.15660.07930.81570.69360.26682.84530.1650.46810.0258-0.0637-0.0682-0.10760.0220.3709-0.11510.3188-0.03030.11980.47230.02540.359259.152519.9102174.3917
191.33330.40550.61261.2553-1.27982.46720.00720.2765-0.0167-0.1237-0.0803-0.1444-0.12730.64680.07040.2355-0.03470.07360.4237-0.0420.306959.209820.5096171.9586
201.2182-0.88410.93441.59250.2462.80790.00010.1637-0.0562-0.1373-0.06110.0662-0.63660.04350.12690.3848-0.11430.04830.3480.00160.392552.296428.5604170.2249
212.3887-1.40361.00862.8243-1.10170.62810.2419-0.32710.01740.1359-0.31090.08810.33210.28580.10130.72890.07580.15750.6632-0.05420.513930.631627.5618182.1543
224.5651.25660.97523.64890.08053.1036-0.4011-0.0609-0.62440.06640.12990.06420.5893-0.82710.40180.8239-0.04760.0980.66020.11770.658246.102227.2192130.4697
230.8778-0.22520.46720.1158-0.08061.60680.19290.0248-0.2443-0.0179-0.0665-0.1207-0.07860.3414-0.0990.26060.02110.0490.30240.00590.267446.162812.1086118.1118
241.618-1.07680.02272.5689-0.08360.69540.0584-0.0701-0.0835-0.30830.04040.1884-0.4688-1.0466-0.00780.43770.15420.04480.43560.00580.303714.835221.9583189.4528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 136 through 282)A136 - 282
2X-RAY DIFFRACTION2chain 'A' and (resid 337 through 365)A337 - 365
3X-RAY DIFFRACTION3chain 'A' and (resid 366 through 445)A366 - 445
4X-RAY DIFFRACTION4chain 'A' and (resid 446 through 477)A446 - 477
5X-RAY DIFFRACTION5chain 'A' and (resid 478 through 499)A478 - 499
6X-RAY DIFFRACTION6chain 'B' and (resid 136 through 282)B136 - 282
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 336)B283 - 336
8X-RAY DIFFRACTION8chain 'B' and (resid 337 through 365)B337 - 365
9X-RAY DIFFRACTION9chain 'B' and (resid 366 through 445)B366 - 445
10X-RAY DIFFRACTION10chain 'B' and (resid 446 through 478)B446 - 478
11X-RAY DIFFRACTION11chain 'C' and (resid 136 through 282)C136 - 282
12X-RAY DIFFRACTION12chain 'C' and (resid 283 through 336)C283 - 336
13X-RAY DIFFRACTION13chain 'C' and (resid 366 through 445)C366 - 445
14X-RAY DIFFRACTION14chain 'C' and (resid 446 through 477)C446 - 477
15X-RAY DIFFRACTION15chain 'C' and (resid 478 through 499)C478 - 499
16X-RAY DIFFRACTION16chain 'D' and (resid 136 through 282)D136 - 282
17X-RAY DIFFRACTION17chain 'D' and (resid 283 through 336)D283 - 336
18X-RAY DIFFRACTION18chain 'D' and (resid 337 through 365)D337 - 365
19X-RAY DIFFRACTION19chain 'D' and (resid 366 through 445)D366 - 445
20X-RAY DIFFRACTION20chain 'D' and (resid 446 through 477)D446 - 477
21X-RAY DIFFRACTION21chain 'E' and (resid 10 through 22 )E10 - 22
22X-RAY DIFFRACTION22chain 'F' and (resid 10 through 25 )F10 - 25
23X-RAY DIFFRACTION23chain 'A' and (resid 283 through 336)A283 - 336
24X-RAY DIFFRACTION24chain 'C' and (resid 337 through 365)C337 - 365

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