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- PDB-4qqk: Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)... -

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Basic information

Entry
Database: PDB / ID: 4qqk
TitleHuman HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) with GMS
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / HRMT1L6 / Protein arginine N-methyltransferase 6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / 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 ...histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / 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 / base-excision repair / protein modification process / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / cellular senescence / histone binding / 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
Chem-37H / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDong, A. / Zeng, H. / He, H. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Luo, M. ...Dong, A. / Zeng, H. / He, H. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Luo, M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem. J. / Year: 2016
Title: Structural basis of arginine asymmetrical dimethylation by PRMT6.
Authors: Wu, H. / Zheng, W. / Eram, M.S. / Vhuiyan, M. / Dong, A. / Zeng, H. / He, H. / Brown, P. / Frankel, A. / Vedadi, M. / Luo, M. / Min, J.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)42,60424
Polymers42,0751
Non-polymers53023
Water3,225179
1
A: Protein arginine N-methyltransferase 6
hetero molecules

A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,20848
Polymers84,1492
Non-polymers1,05946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area4750 Å2
ΔGint-35 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.211, 95.211, 108.359
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) / Gene: PRMT6, HRMT1L6 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q96LA8, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical ChemComp-37H / (5S)-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}-N~6~-carbamimidoyl-L-lysine


Mass: 437.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N9O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 21 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M KSCN, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.88→71.52 Å / Num. obs: 39024 / % possible obs: 100 % / Redundancy: 38.2 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.091 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.918.40.70419250.81100
1.91-1.958.40.50419650.8261100
1.95-1.988.40.55619220.8161100
1.98-2.038.40.41519640.8271100
2.03-2.078.40.35119370.8421100
2.07-2.128.40.30319530.8571100
2.12-2.178.40.24119520.8691100
2.17-2.238.40.20319220.9081100
2.23-2.298.40.16919510.951100
2.29-2.378.40.14819400.911100
2.37-2.458.40.11619650.911100
2.45-2.558.40.09819390.9411100
2.55-2.678.40.08119580.9711100
2.67-2.818.40.06519551.0111100
2.81-2.988.40.05619571.121100
2.98-3.218.40.0519531.4151100
3.21-3.548.30.04719541.9221100
3.54-4.058.30.04319522.0921100
4.05-5.18.10.03119791.6061100
5.1-508.10.02719811.267199.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREP11.0.05phasing
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HC4

4hc4


Resolution: 1.88→71.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.507 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1598 4.1 %RANDOM
Rwork0.1762 ---
obs0.1775 39011 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.7 Å2 / Biso mean: 32.467 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.88→71.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 58 179 2743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192647
X-RAY DIFFRACTIONr_bond_other_d0.0030.022506
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9673599
X-RAY DIFFRACTIONr_angle_other_deg0.8963.0065747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31323.19116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41315431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4961521
X-RAY DIFFRACTIONr_chiral_restr0.080.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_mcbond_it1.9693.0281315
X-RAY DIFFRACTIONr_mcbond_other1.9693.0281315
X-RAY DIFFRACTIONr_mcangle_it2.8824.5281644
LS refinement shellResolution: 1.882→1.931 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 122 -
Rwork0.237 2689 -
all-2811 -
obs--98.87 %

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