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- PDB-7fai: CARM1 bound with compound 9 -

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Basic information

Entry
Database: PDB / ID: 7fai
TitleCARM1 bound with compound 9
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / Histone-arginine methyltransferase CARM1
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-XJ3 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09749259173 Å
AuthorsCao, D.Y. / Li, J. / Xiong, B.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Discovery of Potent CARM1 Inhibitors for Solid Tumor and Cancer Immunology Therapy.
Authors: Zhang, Z. / Guo, Z. / Xu, X. / Cao, D. / Yang, H. / Li, Y. / Shi, Q. / Du, Z. / Guo, X. / Wang, X. / Chen, D. / Zhang, Y. / Chen, L. / Zhou, K. / Li, J. / Geng, M. / Huang, X. / Xiong, B.
History
DepositionJul 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,7178
Polymers152,9144
Non-polymers1,8024
Water4,522251
1
A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6792
Polymers38,2291
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6792
Polymers38,2291
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6792
Polymers38,2291
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6792
Polymers38,2291
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.819, 98.600, 205.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 38228.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical
ChemComp-XJ3 / N'-[[3-[4-(3,5-dimethyl-1,2-oxazol-4-yl)-5-methyl-6-(oxan-4-ylamino)pyrimidin-2-yl]phenyl]methyl]-N-methyl-ethane-1,2-diamine


Mass: 450.576 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H34N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 22-27% PEG 3350, 0.15M sodium malate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.09749259173→60.5308539885 Å / Num. obs: 89925 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.6205243191 Å2 / Rmerge(I) obs: 0.611 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.143 / Num. unique obs: 89925

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IZQ

6izq


Resolution: 2.09749259173→60.53 Å / SU ML: 0.190241207414 / Cross valid method: NONE / σ(F): 1.34359113791 / Phase error: 23.5155768872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231685364763 4485 4.99326438138 %
Rwork0.194254515576 85336 -
obs0.196190884764 89821 99.7335139517 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8189564552 Å2
Refinement stepCycle: LAST / Resolution: 2.09749259173→60.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10726 0 132 251 11109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074628806179611146
X-RAY DIFFRACTIONf_angle_d0.90027380297815110
X-RAY DIFFRACTIONf_chiral_restr0.05594286002291638
X-RAY DIFFRACTIONf_plane_restr0.005865975405641918
X-RAY DIFFRACTIONf_dihedral_angle_d7.059079717926542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0975-2.12130.2403033789511510.19346640412793X-RAY DIFFRACTION99.8304510003
2.1213-2.14630.2657669082821410.1825534097622845X-RAY DIFFRACTION100
2.1463-2.17250.2470368228161310.1897990063492798X-RAY DIFFRACTION99.863620866
2.1725-2.20.2238365426781540.1904589234312831X-RAY DIFFRACTION99.8327759197
2.2-2.22890.2643110713721530.1884159562785X-RAY DIFFRACTION99.9319727891
2.2289-2.25940.2615667929521360.1942244303692832X-RAY DIFFRACTION99.865410498
2.2594-2.29170.2539656813211440.195323982342829X-RAY DIFFRACTION99.9327731092
2.2917-2.32590.2426692400931380.194332225852811X-RAY DIFFRACTION99.9661016949
2.3259-2.36230.2387094877831570.195596136152818X-RAY DIFFRACTION99.9663978495
2.3623-2.4010.2303578631531340.195617272992845X-RAY DIFFRACTION100
2.401-2.44240.2415873512881190.2050686781932822X-RAY DIFFRACTION100
2.4424-2.48680.2595985206131430.2044825522672861X-RAY DIFFRACTION100
2.4868-2.53470.2681254881131300.2034326204782834X-RAY DIFFRACTION100
2.5347-2.58640.2556109661251690.2055433741682818X-RAY DIFFRACTION100
2.5864-2.64260.2640124391361370.2186930681522832X-RAY DIFFRACTION100
2.6426-2.70410.2572554584941530.2121427982992844X-RAY DIFFRACTION99.9666444296
2.7041-2.77170.2327284205021510.2177085871772855X-RAY DIFFRACTION100
2.7717-2.84670.2540839905841580.2265289421332806X-RAY DIFFRACTION100
2.8467-2.93040.2909939878581340.2308630470142870X-RAY DIFFRACTION100
2.9304-3.0250.281002570731370.2282216855842842X-RAY DIFFRACTION100
3.025-3.13310.2899009414791580.2226675303052851X-RAY DIFFRACTION100
3.1331-3.25860.2681929336481460.2125023442692870X-RAY DIFFRACTION100
3.2586-3.40690.2601279588681640.2051107202192837X-RAY DIFFRACTION99.9666888741
3.4069-3.58650.2073698402531560.2016993142741X-RAY DIFFRACTION96.373918829
3.5865-3.81110.2212149694341600.185036276232827X-RAY DIFFRACTION98.6134037636
3.8111-4.10530.1943228140911560.1727442218622875X-RAY DIFFRACTION100
4.1053-4.51830.1711988429121490.156324529652884X-RAY DIFFRACTION100
4.5183-5.17190.188234075881640.1569380674752922X-RAY DIFFRACTION99.8382400518
5.1719-6.51480.2120112374731740.1921835177212930X-RAY DIFFRACTION100
6.5148-60.530.2222593364691880.1865891461363028X-RAY DIFFRACTION98.3486238532

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