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- PDB-1g6q: CRYSTAL STRUCTURE OF YEAST ARGININE METHYLTRANSFERASE, HMT1 -

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Basic information

Entry
Database: PDB / ID: 1g6q
TitleCRYSTAL STRUCTURE OF YEAST ARGININE METHYLTRANSFERASE, HMT1
ComponentsHNRNP ARGININE N-METHYLTRANSFERASE
KeywordsTRANSFERASE / SAM-binding domain / beta-barrel / mixed alpha-beta / hexamer / dimer
Function / homology
Function and homology information


negative regulation of termination of DNA-templated transcription / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine methylation / protein-arginine omega-N asymmetric methyltransferase activity / folic acid biosynthetic process / RMTs methylate histone arginines / Estrogen-dependent gene expression / mRNA export from nucleus / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of transcription elongation by RNA polymerase II ...negative regulation of termination of DNA-templated transcription / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine methylation / protein-arginine omega-N asymmetric methyltransferase activity / folic acid biosynthetic process / RMTs methylate histone arginines / Estrogen-dependent gene expression / mRNA export from nucleus / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of transcription elongation by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich ...Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsWeiss, V.H. / McBride, A.E. / Soriano, M.A. / Filman, D.J. / Silver, P.A. / Hogle, J.M.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: The structure and oligomerization of the yeast arginine methyltransferase, Hmt1.
Authors: Weiss, V.H. / McBride, A.E. / Soriano, M.A. / Filman, D.J. / Silver, P.A. / Hogle, J.M.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Analysis of the yeast arginine methyltransferase Hmt1p/Rmt1p and its in vivo function. Cofactor binding and substrate interactions.
Authors: McBride, A.E. / Weiss, V.H. / Kim, H.K. / Hogle, J.M. / Silver, P.A.
#2: Journal: rna / Year: 1999
Title: Arginine methylation and binding of Hrp1p to the efficiency element for mRNA 3'-end formation.
Authors: valentini, s.r. / weiss, v.h. / silver, p.a.
#3: Journal: Mol.Cell.Biol. / Year: 1996
Title: A novel methyltransferase (Hmt1p) modifies poly(A)+RNA binding proteins.
Authors: henry, m.f. / silver, p.a.
#4: Journal: Genes Dev. / Year: 1998
Title: Arginine methylation facilitates the nuclear export of hnRNP proteins.
Authors: shen, e.c. / Henry, M.F. / Weiss, V.H. / Valentini, S.R. / Silver, P.A. / Lee, M.S.
History
DepositionNov 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Derived calculations
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: HNRNP ARGININE N-METHYLTRANSFERASE
2: HNRNP ARGININE N-METHYLTRANSFERASE
3: HNRNP ARGININE N-METHYLTRANSFERASE
4: HNRNP ARGININE N-METHYLTRANSFERASE
5: HNRNP ARGININE N-METHYLTRANSFERASE
6: HNRNP ARGININE N-METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)226,1566
Polymers226,1566
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
1: HNRNP ARGININE N-METHYLTRANSFERASE
2: HNRNP ARGININE N-METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)75,3852
Polymers75,3852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-31 kcal/mol
Surface area28250 Å2
MethodPISA
3
5: HNRNP ARGININE N-METHYLTRANSFERASE
6: HNRNP ARGININE N-METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)75,3852
Polymers75,3852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-29 kcal/mol
Surface area27840 Å2
MethodPISA
4
3: HNRNP ARGININE N-METHYLTRANSFERASE
4: HNRNP ARGININE N-METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)75,3852
Polymers75,3852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-27 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.100, 129.430, 101.430
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number4
Space group name H-MP1211
Detailshexamer has very approximate 32 symmetry. Monomers exhibit varying degrees of order.

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Components

#1: Protein
HNRNP ARGININE N-METHYLTRANSFERASE


Mass: 37692.613 Da / Num. of mol.: 6 / Fragment: MISSING 20 AMINOACYL RESIDUES FROM N-TERMINUS / Mutation: Q21D, H22Y, N25D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HMT1
Plasmid details: MODIFIED PET15B VECTOR CONTAINING INSERT PRECISSION PROTEASE SITE AFTER HIS TAG (PPS2193)
Plasmid: PPS2193 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) C41
References: UniProt: P38074, Transferases; Transferring one-carbon groups; Methyltransferases

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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: 48.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 microliters of Hmt1 (8mg/ml) in 50 mM Tris, pH 7.0, 50 mM NaCl, 1 mM EDTA, 1 mM DTT + 2 microliters of reservoir:50 mM sodium hepes, pH 7.5, 14% v/v PEG 400, 100 mM CaCl2 + microseeds in 1 ...Details: 2 microliters of Hmt1 (8mg/ml) in 50 mM Tris, pH 7.0, 50 mM NaCl, 1 mM EDTA, 1 mM DTT + 2 microliters of reservoir:50 mM sodium hepes, pH 7.5, 14% v/v PEG 400, 100 mM CaCl2 + microseeds in 1 microliter of 20 mM sodium citrate, pH 5.6, 15% w/v PEG 4000, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-8 mg/mlprotein1drop
250 mMsodium HEPES1reservoir
314 %(v/v)PEG4001reservoir
4100 mM1reservoirCaCl2
520 mMsodium citrate1reservoir
615 %(w/v)PEG40001reservoir
7100 mMammonium acetate + Hmt1 microcrystals1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9784,1.0100,0.9500,0.9788
DetectorType: BRANDEIS / Detector: CCD / Date: Mar 2, 2000 / Details: monochromator
RadiationMonochromator: pair of parallel silicon crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97841
21.011
30.951
40.97881
ReflectionResolution: 2.9→28 Å / Num. all: 91268 / Num. obs: 90403 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.4
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5 / Num. unique all: 8739 / Rsym value: 0.235 / % possible all: 95.9
Reflection
*PLUS
Num. measured all: 277416
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameVersionClassification
SOLVEphasing
MLPHAREphasing
DMmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→28 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: param19x
Details: 65 overlapping resolution-dependent bin scales, plus 1 or 2 grouped B values per aminoacyl residue. With bin-scales present, the refined B's do not correspond to rms displacements. NCS ...Details: 65 overlapping resolution-dependent bin scales, plus 1 or 2 grouped B values per aminoacyl residue. With bin-scales present, the refined B's do not correspond to rms displacements. NCS restraints were applied separately to the SAM-binding domains and the beta-barrel domains, with structurally variable segments of the polypeptide excluded.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 4666 -random
Rwork0.253 ---
all0.253 45634 --
obs0.253 46590 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.9→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15520 0 0 0 15520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_dihedral_angle_d25.06
X-RAY DIFFRACTIONx_improper_angle_d1.29
LS refinement shellResolution: 2.9→2.97 Å /
RfactorNum. reflection
Rfree0.362 87
Rwork0.333 -
obs-816
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29

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