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- PDB-9vkf: Crystal structure of yeast arginine N-methyltransferase 1,HMT1 -

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Basic information

Entry
Database: PDB / ID: 9vkf
TitleCrystal structure of yeast arginine N-methyltransferase 1,HMT1
ComponentsProtein arginine N-methyltransferase 1
KeywordsGENE REGULATION / homo dimer / Protein arginine N-methyltransferase 1 / HMT1 / GENE REGULATION. / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of termination of DNA-templated transcription / protein-arginine omega-N monomethyltransferase activity / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / protein-arginine N-methyltransferase activity / RMTs methylate histone arginines / Protein methylation / folic acid biosynthetic process / histone methyltransferase activity / Estrogen-dependent gene expression ...negative regulation of termination of DNA-templated transcription / protein-arginine omega-N monomethyltransferase activity / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / protein-arginine N-methyltransferase activity / RMTs methylate histone arginines / Protein methylation / folic acid biosynthetic process / histone methyltransferase activity / Estrogen-dependent gene expression / mRNA export from nucleus / positive regulation of transcription elongation by RNA polymerase II / methylation / chromatin remodeling / regulation of DNA-templated transcription / identical protein binding / nucleus
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsYang, X.Y. / Zhou, Y.H. / Shang, X.C. / Liu, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271309 China
CitationJournal: To Be Published
Title: Crystal structure of yeast arginine N-methyltransferase 1,HMT1
Authors: Liu, Y.L. / Yang, X.Y. / Zhou, Y.H. / Shang, X.C.
History
DepositionJun 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 1
B: Protein arginine N-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)75,3592
Polymers75,3592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-31 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.670, 84.670, 97.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein arginine N-methyltransferase 1 / Major type I protein arginine N-methyltransferase / Type I PRMT / hnRNP arginine N-methyltransferase


Mass: 37679.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HMT1, ODP1, RMT1, YBR034C, YBR0320 / Production host: Escherichia coli (E. coli)
References: UniProt: P38074, type I protein arginine methyltransferase
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.15 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.85→42.33 Å / Num. obs: 18335 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.268 / Net I/σ(I): 15.2
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 1.13 / Num. unique obs: 1379 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→34.33 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 811 4.43 %
Rwork0.2349 --
obs0.2349 18303 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 0 0 4642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044811
X-RAY DIFFRACTIONf_angle_d0.696501
X-RAY DIFFRACTIONf_dihedral_angle_d14.9681725
X-RAY DIFFRACTIONf_chiral_restr0.046727
X-RAY DIFFRACTIONf_plane_restr0.003816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.36141690.32332901X-RAY DIFFRACTION100
3.03-3.260.36351280.27772932X-RAY DIFFRACTION100
3.26-3.590.34681580.25442901X-RAY DIFFRACTION100
3.59-4.110.2761280.23412881X-RAY DIFFRACTION100
4.11-5.170.20611080.18542974X-RAY DIFFRACTION100
5.18-34.330.26311200.21872903X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.6287 Å / Origin y: 2.3875 Å / Origin z: -28.291 Å
111213212223313233
T0.2656 Å20.0092 Å20.0379 Å2-0.5779 Å20.0276 Å2--0.4542 Å2
L0.5002 °2-0.2246 °2-0.1535 °2-1.0588 °20.8564 °2--2.0433 °2
S-0.0568 Å °0.1403 Å °0.0104 Å °-0.0335 Å °0.1694 Å °-0.0929 Å °-0.155 Å °0.406 Å °-0.1177 Å °
Refinement TLS groupSelection details: all

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