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- PDB-7okp: Crystal structure of mouse CARM1 in complex with histone H3_13-22... -

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Basic information

Entry
Database: PDB / ID: 7okp
TitleCrystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated
Components
  • Histone H3.3H3F3A
  • Histone-arginine methyltransferase CARM1
KeywordsTRANSCRIPTION / protein arginine N-methyltransferase / PRMT / CARM1 / transition state mimics
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 / nucleosomal DNA binding / 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 / RNA polymerase II core promoter sequence-specific DNA binding / intracellular estrogen receptor signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / intracellular steroid hormone receptor signaling pathway / response to cAMP / protein localization to chromatin / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / nuclear receptor coactivator activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / methylation / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / 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 / extracellular exosome / extracellular region / 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
MALONATE ION / Chem-QVR / Histone H3.3 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMay 18, 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 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

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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 H3.3
F: Histone H3.3
G: Histone H3.3
H: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,11917
Polymers172,5008
Non-polymers1,6199
Water7,584421
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
E: Histone H3.3
F: Histone H3.3
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
E: Histone H3.3
F: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,81314
Polymers172,5008
Non-polymers1,3136
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area23310 Å2
ΔGint-107 kcal/mol
Surface area49640 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
G: Histone H3.3
H: Histone H3.3
hetero molecules

C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
G: Histone H3.3
H: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,42520
Polymers172,5008
Non-polymers1,92512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area24260 Å2
ΔGint-94 kcal/mol
Surface area49660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.909, 99.580, 208.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 H3.3 / H3F3A


Mass: 1139.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride

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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
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→46.11 Å / Num. obs: 77281 / % possible obs: 97.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 34.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 0.85 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4317 / CC1/2: 0.69 / Rpim(I) all: 0.406 / Rrim(I) all: 0.809 / Χ2: 0.65 / % possible all: 93.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless1.12.8data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3


Resolution: 2.2→45.32 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 3821 4.97 %
Rwork0.2107 73125 -
obs0.213 76946 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.41 Å2 / Biso mean: 52.6059 Å2 / Biso min: 22.79 Å2
Refinement stepCycle: final / Resolution: 2.2→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11707 0 45 425 12177
Biso mean--64.81 44.42 -
Num. residues----1457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.37131440.31692556270093
2.23-2.260.33351410.31182594273593
2.26-2.290.35371430.29792597274094
2.29-2.320.34681270.29342603273094
2.32-2.360.36541250.29042623274895
2.36-2.390.32321270.28052640276795
2.39-2.430.33861470.26932642278994
2.43-2.470.32451490.26082615276496
2.47-2.520.31781200.25672650277095
2.52-2.570.35121410.2622676281795
2.57-2.620.31541380.25692653279196
2.62-2.680.28571470.24272681282896
2.68-2.740.31091310.23712654278596
2.74-2.810.26591390.23862717285697
2.81-2.880.28791350.23012712284797
2.88-2.970.31571270.23592710283797
2.97-3.060.25951440.23092708285297
3.06-3.170.28861570.23452708286597
3.17-3.30.32221450.22482731287697
3.3-3.450.25091260.20472762288897
3.45-3.630.21581330.19092779291298
3.63-3.860.21571570.17572789294699
3.86-4.160.19541620.16522806296899
4.16-4.570.19571480.15312783293199
4.57-5.240.2051350.15262873300899
5.24-6.590.22411590.196128773036100
6.6-45.320.21511740.2032986316098
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)
11.6903-0.2884-0.15191.16010.19412.12780.1403-0.1890.31190.1824-0.1648-0.0978-0.47820.37770.04560.4765-0.2460.06250.54120.00940.333755.17939.73134.414
20.7578-0.04960.4674-0.02210.0620.80860.2453-0.0077-0.10790.058-0.1234-0.05820.01640.3177-0.11150.2051-0.0243-0.00380.4480.00770.250846.24211.836117.991
30.0607-0.0252-0.02392.50610.97911.3673-0.11890.07340.0569-0.09110.0685-0.3845-0.19440.48430.02150.2717-0.11790.00710.62660.07160.340161.71320.184122.863
40.53390.5024-0.24572.5586-0.16491.04680.05330.03-0.0146-0.1762-0.0487-0.3204-0.08040.56110.00160.2207-0.0660.02170.61240.04360.275662.10818.416121.267
50.07830.0420.18613.08980.06471.50650.08490.0676-0.1231-0.295-0.1540.0106-0.11880.20420.04340.2169-0.06410.01060.58950.03190.326353.42517.287114.885
63.2189-0.6972-1.63982.92570.28870.79-0.1237-0.1977-0.2210.47350.0635-0.0509-0.87110.68080.21110.4529-0.1024-0.02110.8044-0.02420.374460.71-3.378134.163
71.32130.0977-0.24252.13970.27962.31290.14190.36070.1205-0.1979-0.07060.112-0.3009-0.0945-0.07390.22750.07940.03150.48820.04840.226519.86419.744114.801
81.46130.937-0.46660.68440.12580.570.2807-0.41750.17020.2726-0.25230.1199-0.3257-0.0562-0.03770.4609-0.06060.06190.5378-0.01580.271433.01326.556144.478
93.597-1.48591.42062.2767-0.7675.01990.3559-0.4908-0.06710.0862-0.09920.28670.2949-0.4584-0.21480.2667-0.13460.0310.419-0.02970.260817.35321.15138.134
100.8732-0.27410.52050.94450.21922.04160.0602-0.39810.03830.2228-0.07690.1139-0.115-0.47320.01830.2575-0.0130.07640.58360.00830.280717.15721.731140.665
110.8134-0.6163-0.26240.91860.7252.10640.0633-0.20350.08540.07630.1105-0.1963-0.31920.2249-0.21650.3415-0.0730.08140.4035-0.0060.351425.21128.925142.077
122.1977-0.3167-0.28011.7586-0.80132.2910.0928-0.01270.35490.1865-0.0257-0.0597-0.7204-0.0442-0.08290.5822-0.03430.10890.338-0.02490.292522.71440.907177.815
131.3680.01040.54010.4323-0.64180.89320.0573-0.1315-0.21450.27210.03980.1245-0.2696-0.1247-0.07730.4022-0.04640.07180.3062-0.03430.262429.6212.523194.432
141.1026-0.5002-0.34212.2423-0.30010.77870.0583-0.0485-0.17260.0322-0.0610.229-0.1984-0.17640.02020.3953-0.08420.0660.488-0.05330.35414.79122.137189.437
151.3209-0.5094-0.39361.8848-0.24762.79430.001-0.2223-0.11690.4102-0.01620.2715-0.1203-0.49070.01250.4649-0.0960.11180.3758-0.0470.322414.16320.323190.993
161.76190.11750.89654.6623-0.64581.7915-0.1492-0.2116-0.12440.18850.06690.17940.0003-0.07190.08860.3648-0.05730.08870.4766-0.04810.284622.72618.567197.415
171.2471-1.2033-1.65643.06070.24692.98470.3342-0.211-0.0529-0.3356-0.3515-0.1696-0.7105-0.53310.09280.4883-0.04150.0120.78310.15070.467314.111-1.496178.23
182.24590.1087-0.05371.7383-0.01341.68650.2019-0.33840.02620.3404-0.1107-0.1921-0.33990.1374-0.09450.5196-0.24650.05670.4359-0.04180.311756.66118.282197.631
191.6282-1.11860.54250.827-0.24280.23280.11650.51050.0376-0.0355-0.2139-0.1342-0.29560.26960.07420.5133-0.13830.08830.53450.00330.304943.96326.207167.894
204.47140.55951.88740.61360.00263.37520.23110.98870.1646-0.0991-0.0688-0.16260.12830.4191-0.16140.4442-0.0430.14730.45770.02180.323459.03419.731174.198
211.51390.33760.591.6385-0.63581.37920.07430.580.0961-0.1881-0.1267-0.156-0.21660.550.03650.3844-0.10480.07670.6293-0.01060.273559.20620.146171.904
222.98950.5535-1.80830.8265-0.65995.03770.39680.34310.08540.1508-0.0649-0.0176-0.9267-0.026-0.37580.4803-0.11730.02050.45140.06260.371452.05327.761170.138
231.87970.09250.65862.1630.11051.20970.1994-0.5522-0.10960.4923-0.03110.14120.1446-0.2697-0.10160.3619-0.12760.04680.67110.00910.290247.65526.611131.916
243.6236-1.02111.73651.916-1.92754.61910.35120.0431-0.0714-0.0519-0.1706-0.4207-0.00041.3083-0.20170.3544-0.0087-0.0070.6683-0.00250.360930.3718.98125.875
251.5475-0.6958-0.42772.85280.19920.60020.0848-0.07590.2048-0.3003-0.4288-0.146-0.30360.33780.30580.5651-0.11740.05970.4022-0.07610.335329.40927.415180.497
261.52080.21410.66091.22640.97551.97360.06350.0592-0.1390.13340.11740.16950.3151-0.7595-0.21430.5197-0.1333-0.0060.64540.08110.321346.13618.435186.609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 135:282 )A135 - 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 478:497 )A478 - 497
7X-RAY DIFFRACTION7( CHAIN B AND RESID 135:282 )B135 - 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 136:282 )C136 - 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 478:497 )C478 - 497
18X-RAY DIFFRACTION18( CHAIN D AND RESID 135:282 )D135 - 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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  • 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

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