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- PDB-4g56: Crystal Structure of full length PRMT5/MEP50 complexes from Xenop... -

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Basic information

Entry
Database: PDB / ID: 4g56
TitleCrystal Structure of full length PRMT5/MEP50 complexes from Xenopus laevis
Components
  • Hsl7 protein
  • MGC81050 protein
KeywordsTRANSFERASE / protein arginine methyltransferase / protein complexes / histone methylation / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / histone H4R3 methyltransferase activity / : / positive regulation of proteasomal protein catabolic process / methylosome / mitotic DNA replication checkpoint signaling ...histone H2AR3 methyltransferase activity / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / histone H4R3 methyltransferase activity / : / positive regulation of proteasomal protein catabolic process / methylosome / mitotic DNA replication checkpoint signaling / regulation of mitotic nuclear division / E-box binding / histone methyltransferase complex / circadian regulation of gene expression / transcription corepressor activity / methylation / cell division / regulation of DNA-templated transcription / Golgi apparatus / nucleus / cytosol
Similarity search - Function
: / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 ...: / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Divalent-metal-dependent TIM barrel enzymes / YVTN repeat-like/Quinoprotein amine dehydrogenase / Vaccinia Virus protein VP39 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Distorted Sandwich / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHo, M. / Wilczek, C. / Bonanno, J. / Shechter, D. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Plos One / Year: 2013
Title: Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity
Authors: Ho, M.C. / Wilczek, C. / Bonanno, J.B. / Xing, L. / Seznec, J. / Matsui, T. / Carter, L.G. / Onikubo, T. / Kumar, P.R. / Chan, M.K. / Brenowitz, M. / Cheng, R.H. / Reimer, U. / Almo, S.C. / Shechter, D.
History
DepositionJul 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Derived calculations
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3Sep 4, 2013Group: Database references
Revision 1.4Sep 11, 2013Group: Other
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software
Revision 1.6Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Hsl7 protein
B: MGC81050 protein
C: Hsl7 protein
D: MGC81050 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,9416
Polymers229,1724
Non-polymers7692
Water1629
1
A: Hsl7 protein
B: MGC81050 protein
C: Hsl7 protein
D: MGC81050 protein
hetero molecules

A: Hsl7 protein
B: MGC81050 protein
C: Hsl7 protein
D: MGC81050 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,88212
Polymers458,3458
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area30530 Å2
ΔGint-78 kcal/mol
Surface area138580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.856, 101.935, 125.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hsl7 protein / Methyltransferase Hsl7


Mass: 75713.453 Da / Num. of mol.: 2 / Fragment: UNP residues 2-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hsl7, PRMT5 / Plasmid: pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6NUA1
#2: Protein MGC81050 protein


Mass: 38872.746 Da / Num. of mol.: 2 / Fragment: UNP residues 2-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: MEP50, MGC81050, wdr77 / Plasmid: pSPL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6NUD0
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.6 % / Mosaicity: 0.135 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 35%MPD, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 49960 / Num. obs: 49895 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.3 % / Rmerge(I) obs: 0.15 / Χ2: 1.067 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0660.89848881.062199.9
3.06-3.186.20.65349411.083199.9
3.18-3.326.30.46749211.0961100
3.32-3.56.40.32649481.0991100
3.5-3.726.20.22549451.0991100
3.72-46.30.16549621.1011100
4-4.416.60.11349891.0631100
4.41-5.046.40.08550231.061100
5.04-6.356.50.08750581.0431100
6.35-506.10.05552650.964199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→37.898 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.794 / SU ML: 0.35 / σ(F): 1.42 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 1957 4.02 %RANDOM
Rwork0.2178 ---
obs0.2201 48735 97.62 %-
all-49960 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.52 Å2 / Biso mean: 65.2201 Å2 / Biso min: 19.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.404 Å
Refinement stepCycle: LAST / Resolution: 2.95→37.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14413 0 52 9 14474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214853
X-RAY DIFFRACTIONf_angle_d0.56820189
X-RAY DIFFRACTIONf_chiral_restr0.0392198
X-RAY DIFFRACTIONf_plane_restr0.0022597
X-RAY DIFFRACTIONf_dihedral_angle_d11.1015396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.95-3.02330.34541240.3046305091
3.0233-3.1050.2921330.2849319094
3.105-3.19630.33311380.2664324196
3.1963-3.29940.29981410.2665325196
3.2994-3.41720.32891380.255326797
3.4172-3.5540.33281370.2396330698
3.554-3.71560.28091420.2227335998
3.7156-3.91130.31291410.2212336399
3.9113-4.15610.25221390.2012336499
4.1561-4.47650.27681430.1924341899
4.4765-4.92610.24431410.1804341799
4.9261-5.63690.23141430.1952344099
5.6369-7.09430.28671440.22363474100
7.0943-37.90070.23551530.19823638100

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