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- PDB-7u9i: Co-crystal structure of human CARM1 in complex with MT556 inhibitor -

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Basic information

Entry
Database: PDB / ID: 7u9i
TitleCo-crystal structure of human CARM1 in complex with MT556 inhibitor
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / MTase / Histone arginine methyltransferase / PRMT4 / CARM1 / SGC / Structural Genomics / Structural Genomics Consortium / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / 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 / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / RMTs methylate histone arginines / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / 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
Chem-44T / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsZeng, H. / Perveen, S. / Dong, A. / Hutchinson, A. / Seitova, A. / Gibson, E. / Hajian, T. / Li, Y. / Gao, Y.D. / Schneider, S. ...Zeng, H. / Perveen, S. / Dong, A. / Hutchinson, A. / Seitova, A. / Gibson, E. / Hajian, T. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Vedadi, M. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Co-crystal structure of human CARM1 in complex with MT556 inhibitor
Authors: Zeng, H. / Perveen, S. / Dong, A. / Hutchinson, A. / Seitova, A. / Gibson, E. / Hajian, T. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. ...Authors: Zeng, H. / Perveen, S. / Dong, A. / Hutchinson, A. / Seitova, A. / Gibson, E. / Hajian, T. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Vedadi, M. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionMar 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,01218
Polymers78,0672
Non-polymers94516
Water3,765209
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-22 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.269, 98.197, 206.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 39033.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical ChemComp-44T / 7-[5-S-(4-{[(4-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 472.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.41 Å3/Da / Density % sol: 49.06 % / Mosaicity: 0.35 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M di-Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→44.35 Å / Num. obs: 49481 / % possible obs: 97 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Net I/σ(I): 13.7 / Num. measured all: 258148 / Scaling rejects: 114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0550.8361885237710.7130.3910.9271.899.9
8.94-44.355.30.02627965320.9980.0120.02956.685.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DXJ

5dxj


Resolution: 2→40.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.383 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2428 4.9 %RANDOM
Rwork0.2033 ---
obs0.2064 47040 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.34 Å2 / Biso mean: 30.477 Å2 / Biso min: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2--1.19 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 80 210 5460
Biso mean--28.88 35.3 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135419
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174869
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6347366
X-RAY DIFFRACTIONr_angle_other_deg1.3151.58111271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74623.022268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46715860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7331521
X-RAY DIFFRACTIONr_chiral_restr0.070.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021183
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 178 -
Rwork0.279 3589 -
all-3767 -
obs--99.79 %

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