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- PDB-7qph: Crystal structure of mouse CARM1 in complex with histone H3_22-31... -

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Basic information

Entry
Database: PDB / ID: 7qph
TitleCrystal structure of mouse CARM1 in complex with histone H3_22-31 K27 acetylated
Components
  • Histone H3 22-31 K27 acetylated
  • Histone-arginine methyltransferase CARM1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of growth plate cartilage chondrocyte proliferation / histone H3R26 methyltransferase activity / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase ...regulation of growth plate cartilage chondrocyte proliferation / histone H3R26 methyltransferase activity / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / Estrogen-dependent gene expression / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / histone methyltransferase activity / nuclear replication fork / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of fat cell differentiation / estrogen receptor signaling pathway / protein localization to chromatin / 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-QVR / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 22-31 K27 acetylated
H: Histone H3 22-31 K27 acetylated
G: Histone H3 22-31 K27 acetylated
F: Histone H3 22-31 K27 acetylated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,75013
Polymers167,5798
Non-polymers1,1715
Water11,548641
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.343, 99.184, 208.443
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-553-

HOH

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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: Protein/peptide
Histone H3 22-31 K27 acetylated


Mass: 1044.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 3350, 0.2M ammonium sulfate, 0.1M Tris HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→48.25 Å / Num. obs: 123546 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.572 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6017 / CC1/2: 0.546 / Rpim(I) all: 0.742 / Rrim(I) all: 1.744 / % possible all: 99.3

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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: 1.9→48.25 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 6145 4.98 %
Rwork0.1832 117216 -
obs0.1845 123361 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.95 Å2 / Biso mean: 50.9468 Å2 / Biso min: 22.85 Å2
Refinement stepCycle: final / Resolution: 1.9→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11216 0 417 641 12274
Biso mean--69.45 47.69 -
Num. residues----1372
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 (%)
1.9-1.920.38182280.34393808403699
1.92-1.940.34832050.314138734078100
1.94-1.970.32421810.299738384019100
1.97-1.990.29392050.280438524057100
1.99-2.020.32981920.254438704062100
2.02-2.050.27892200.239338674087100
2.05-2.080.27632310.227938414072100
2.08-2.110.25291780.214438874065100
2.11-2.140.23541880.203338614049100
2.14-2.170.23112100.196938844094100
2.17-2.210.24462060.20538784084100
2.21-2.250.23692190.199938584077100
2.25-2.30.22782070.190638594066100
2.3-2.340.23191930.196939104103100
2.34-2.390.24921840.198539104094100
2.39-2.450.20812080.193338714079100
2.45-2.510.23342020.187539274129100
2.51-2.580.22522030.18238954098100
2.58-2.650.18911960.183739124108100
2.65-2.740.22572060.178638824088100
2.74-2.840.212000.193339274127100
2.84-2.950.24181900.199839204110100
2.95-3.090.24222090.210139234132100
3.09-3.250.22372080.192539304138100
3.25-3.450.21741990.183439594158100
3.45-3.720.21371970.170239534150100
3.72-4.090.16522270.149139374164100
4.09-4.680.14912090.133640084217100
4.68-5.90.18011970.149940554252100
5.9-48.250.18952470.19644121436898
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)
12.3053-1.0018-0.36511.94750.33922.1885-0.10720.01720.39820.1137-0.0031-0.1256-0.20470.04770.11460.3394-0.096-0.02870.27730.00490.29755.079440.378134.6211
21.24980.11730.6945-0.05580.15631.0250.10790.0087-0.07290.0633-0.03940.00990.07020.1133-0.07950.2323-0.01980.0060.21510.00360.308946.270412.1056118.4945
31.3975-0.02550.39722.98111.07381.3540.02170.03570.05370.21780.0095-0.1255-0.07740.1833-0.03470.2938-0.10890.02790.35460.01540.267161.575520.9606123.1295
40.6065-0.0253-0.28392.39380.33461.7008-0.01130.04170.0216-0.0531-0.024-0.25320.05930.2520.05160.2307-0.05370.00520.30310.04660.291762.228318.985121.6194
52.6058-1.20130.36653.50660.80791.1192-0.0081-0.006-0.2560.3112-0.20970.27910.2532-0.27320.20180.3438-0.11830.07890.28490.01860.303553.324117.4764115.7373
62.1329-0.4009-0.02040.94940.96213.58150.25270.13860.2744-0.1633-0.0480.0179-0.5121-0.3347-0.1930.36040.07680.06220.25260.08420.307719.657919.3707115.0731
71.12060.86090.29860.63180.08320.85020.2668-0.16250.0890.2955-0.15260.0706-0.1683-0.0284-0.10840.46210.0050.05460.3588-0.02050.293232.847127.1107144.6193
83.9676-0.17311.20690.89560.78784.23010.2365-0.42470.10050.0844-0.09710.12020.1826-0.4417-0.14570.33690.00250.07270.31140.00490.284917.241621.5373138.2866
91.34880.23830.9691.02971.52633.13440.1365-0.29010.0040.1835-0.04040.03990.0842-0.5132-0.0890.3697-0.00230.04790.37690.07920.286717.121822.1802140.6859
101.508-0.33590.66012.0552-0.12694.05510.33470.02360.0765-0.2313-0.1066-0.4047-0.48650.0124-0.19660.3917-0.05080.07080.3427-0.0080.385524.899129.5468142.2261
113.49120.263-0.97691.7593-0.56972.7940.14120.11790.6280.152-0.02580.0023-0.7012-0.1337-0.11070.54730.0420.060.32620.01950.343522.516441.381178.0749
121.7347-0.75260.39290.03660.2110.74560.1270.00910.0891-0.0244-0.1054-0.0479-0.0171-0.143-0.05110.2906-0.03020.04490.24090.00970.327929.80112.6042194.3795
132.2885-0.23780.11552.7177-0.721.56490.03340.0837-0.0945-0.0539-0.06980.1623-0.1691-0.21640.01610.26070.03890.07490.3185-0.01530.232414.967322.2563189.4394
141.4453-0.2413-0.70632.1419-0.4421.99170.02710.0518-0.06720.1299-0.0770.2369-0.0763-0.33950.0550.24940.00980.04850.3126-0.06630.287614.159620.4658190.8991
154.24831.0237-0.16073.7404-1.08462.5779-0.03910.2503-0.2449-0.1393-0.1047-0.22780.0896-0.0020.10540.34090.02760.06750.2957-0.04050.328222.885418.4701196.885
161.79080.2379-0.29661.4567-0.57962.03460.1068-0.08920.21940.139-0.01110.0402-0.29310.0811-0.10040.3019-0.05230.04110.2655-0.04540.296456.964618.1045197.8234
171.34-0.99320.50550.5224-0.27410.3640.14870.29990.0441-0.1804-0.1125-0.0523-0.0532-0.0127-0.02880.399-0.04640.02540.47990.03260.311444.093926.7855168.1623
183.3871-0.24921.07761.0319-0.37883.76420.15740.4490.071-0.2011-0.0445-0.05190.28090.2086-0.11380.3268-0.01870.03640.29680.0480.271759.292220.2344174.4154
191.3301-0.230.96751.154-1.51942.4990.08310.43720.0546-0.213-0.10090.0089-0.01760.4080.01490.3576-0.03150.02080.4063-0.03170.286159.410120.8898172.0727
202.184-0.34150.19391.9918-0.05724.83770.15160.117-0.0177-0.0531-0.04670.3779-0.1479-0.2544-0.13530.3074-0.0086-0.04520.33130.00840.337952.1428.5366170.5444
212.01692.37962.31116.04690.92867.2249-0.1710.1911-1.2132-1.1557-0.0640.93151.7443-0.80970.15870.6035-0.1160.0320.4758-0.05240.65548.813731.03130.7013
222.0080.13520.66247.1498-1.21952.00860.2479-1.2273-0.1160.90830.2696-0.0059-0.44110.7915-0.50410.51430.05310.0350.6445-0.02590.58627.599621.2186123.5697
232.0142-0.83143.20622.0013-1.44647.09630.2957-0.0176-1.44780.0144-0.6277-0.41890.62080.64080.30920.5938-0.07690.1210.487-0.00730.700628.305731.6157181.9287
246.1677-1.6372-0.50266.0409-0.28466.75120.47951.03680.1612-1.2141-0.0730.2439-0.5691-0.658-0.42180.54180.01580.00680.49350.06290.428648.955620.4892189.1986
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 136:282)B136 - 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 446:478)B446 - 478
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 446:478)D446 - 478
21X-RAY DIFFRACTION21(chain E and resid 24:27)E24 - 27
22X-RAY DIFFRACTION22(chain F and resid 24:27)F24 - 27
23X-RAY DIFFRACTION23(chain G and resid 24:27)G24 - 27
24X-RAY DIFFRACTION24(chain H and resid 24:27)H24 - 27

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