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- PDB-5wcf: Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) -

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Basic information

Entry
Database: PDB / ID: 5wcf
TitleHuman HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / HRMT1L6 / methyltransferase / MTLLE1441 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / base-excision repair / protein modification process / RMTs methylate histone arginines / cellular senescence / histone binding / methylation / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / 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 ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Chem-A0S / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsDong, A. / Zeng, H. / Hutch, A. / Seitova, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with MTLLE1441
Authors: Zeng, H. / Dong, A. / Hutch, A. / Seitova, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0244
Polymers42,0751
Non-polymers9503
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint3 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.721, 94.721, 108.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Protein arginine N-methyltransferase 6 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N- ...Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 42074.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: PRMT6, HRMT1L6 / Plasmid: pFBOH-MHL / Production host: unidentified baculovirus
References: UniProt: Q96LA8, type I protein arginine methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-A0S / (5R)-4-(5-bromofuran-2-carbonyl)-5-(4-fluorophenyl)-7-methyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one


Mass: 443.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16BrFN2O3
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.55 % / Mosaicity: 0.365 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 15% PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 33057 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Χ2: 1.639 / Net I/σ(I): 13 / Num. measured all: 253023
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.017.70.90716490.7580.3510.9730.92100
2.01-2.057.60.7730.8190.2990.8290.951100
2.05-2.097.70.6250.8690.2420.671.009100
2.09-2.137.70.4960.9030.1920.5320.966100
2.13-2.187.70.4070.9280.1570.4370.992100
2.18-2.237.70.3540.950.1370.3791.033100
2.23-2.297.70.3040.9570.1170.3261.136100
2.29-2.357.70.2440.9740.0940.2621.058100
2.35-2.427.70.2060.9830.080.2211.114100
2.42-2.497.70.1770.9870.0680.191.276100
2.49-2.587.70.1510.990.0580.1621.464100
2.58-2.697.70.130.9910.050.141.715100
2.69-2.817.70.1050.9940.0410.1131.742100
2.81-2.967.80.0790.9970.0310.0851.657100
2.96-3.147.70.0620.9980.0240.0671.655100
3.14-3.397.60.0620.9970.0240.0662.587100
3.39-3.737.40.0580.9980.0230.0633.552100
3.73-4.267.50.0470.9980.0180.0513.354100
4.26-5.377.60.0370.9990.0140.0392.563100
5.37-507.50.0330.9990.0130.0352.12799.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HC4

4hc4


Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.697 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 966 2.9 %RANDOM
Rwork0.1997 ---
obs0.1999 32078 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.06 Å2 / Biso mean: 45.069 Å2 / Biso min: 26.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 62 102 2623
Biso mean--46.48 48.08 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192737
X-RAY DIFFRACTIONr_bond_other_d0.0020.022541
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9673725
X-RAY DIFFRACTIONr_angle_other_deg0.90435853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33322.456114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7115447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.751524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
LS refinement shellResolution: 1.984→2.036 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 76 -
Rwork0.279 2268 -
all-2344 -
obs--96.78 %

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