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- PDB-6v0n: PRMT5 bound to PBM peptide from Riok1 -

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Basic information

Entry
Database: PDB / ID: 6v0n
TitlePRMT5 bound to PBM peptide from Riok1
Components
  • Methylosome protein 50WD repeat-containing protein 77
  • Protein arginine N-methyltransferase 5
  • Riok1 PBM peptide
KeywordsTRANSFERASE/SPLICING / methylation / epigenetics / splicing / SDMA / TRANSFERASE-SPLICING complex
Function / homology
Function and homology information


methyltransferase complex / positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances ...methyltransferase complex / positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / positive regulation of rRNA processing / epithelial cell proliferation involved in prostate gland development / histone arginine N-methyltransferase activity / methylosome / protein-arginine N-methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / : / endothelial cell activation / histone H3 methyltransferase activity / preribosome, small subunit precursor / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / regulation of mitotic nuclear division / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal snRNP assembly / ribonucleoprotein complex binding / maturation of SSU-rRNA / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / liver regeneration / methyltransferase activity / DNA-templated transcription termination / circadian regulation of gene expression / ribosomal small subunit biogenesis / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / hydrolase activity / chromatin remodeling / protein heterodimerization activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rio1 / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / RIO1 family / Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain ...Serine/threonine-protein kinase Rio1 / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / RIO1 family / Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
SINEFUNGIN / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77 / Serine/threonine-protein kinase RIO1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsMcMIllan, B.J. / Raymond, D.D.
CitationJournal: Mol.Cell / Year: 2021
Title: Molecular basis for substrate recruitment to the PRMT5 methylosome.
Authors: Mulvaney, K.M. / Blomquist, C. / Acharya, N. / Li, R. / Ranaghan, M.J. / O'Keefe, M. / Rodriguez, D.J. / Young, M.J. / Kesar, D. / Pal, D. / Stokes, M. / Nelson, A.J. / Jain, S.S. / Yang, A. ...Authors: Mulvaney, K.M. / Blomquist, C. / Acharya, N. / Li, R. / Ranaghan, M.J. / O'Keefe, M. / Rodriguez, D.J. / Young, M.J. / Kesar, D. / Pal, D. / Stokes, M. / Nelson, A.J. / Jain, S.S. / Yang, A. / Mullin-Bernstein, Z. / Columbus, J. / Bozal, F.K. / Skepner, A. / Raymond, D. / LaRussa, S. / McKinney, D.C. / Freyzon, Y. / Baidi, Y. / Porter, D. / Aguirre, A.J. / Ianari, A. / McMillan, B. / Sellers, W.R.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Sep 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Riok1 PBM peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2234
Polymers110,8413
Non-polymers3811
Water9,170509
1
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,48512
Polymers437,9598
Non-polymers1,5264
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area30390 Å2
ΔGint-93 kcal/mol
Surface area135030 Å2
MethodPISA
2
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Riok1 PBM peptide
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Riok1 PBM peptide
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Riok1 PBM peptide
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Riok1 PBM peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,89016
Polymers443,36512
Non-polymers1,5264
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
MethodPISA
Unit cell
Length a, b, c (Å)105.960, 139.410, 179.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-105-

HOH

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Components

#1: Protein Protein arginine N-methyltransferase 5 / 72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / ...72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / Shk1 kinase-binding protein 1 homolog / SKB1Hs


Mass: 72766.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein Methylosome protein 50 / WD repeat-containing protein 77 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / p44/Mep50


Mass: 36723.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BQA1
#3: Protein/peptide Riok1 PBM peptide


Mass: 1351.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BRS2*PLUS
#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% PEG 3350 200 mM ammonium sulfate 0.05% w/v dodecyl-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.11→47.75 Å / Num. obs: 76646 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0119 / Net I/σ(I): 10.65
Reflection shellResolution: 2.11→2.22 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1533 / CC1/2: 0.436 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GQB

4gqb


Resolution: 2.11→47.75 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3833 5 %RANDOM
Rwork0.203 ---
obs0.204 76646 99.9 %-
Displacement parametersBiso max: 142.33 Å2 / Biso mean: 60.05 Å2 / Biso min: 32.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.8265 Å20 Å20 Å2
2---16.8607 Å20 Å2
3---13.0342 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.11→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 27 509 7904
Biso mean--52.39 59.48 -
Num. residues----930
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2565SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1303HARMONIC5
X-RAY DIFFRACTIONt_it7609HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion977SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8554SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7609HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10372HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion17.7
LS refinement shellResolution: 2.11→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3904 77 5.02 %
Rwork0.3481 1456 -
all0.3503 1533 -
obs--97.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0663-0.11-0.01831.12830.19340.67140.01670.04690.0091-0.0689-0.0251-0.1418-0.12560.16180.00840.0491-0.0420.01010.2513-0.00780.1759-32.339-62.195-19.545
21.4772-0.3484-0.26951.54370.00322.6544-0.07990.2611-0.2945-0.245-0.0391-0.13370.6480.01450.11910.40770.08890.08670.3439-0.11790.2897-24.865-111.927-37.75
36.76840.03774.656910.433-1.34916.4853-0.05210.20330.1292-0.08850.02-0.5044-0.29130.35910.0321-0.0512-0.02660.3130.3072-0.0710.5709-2.542-74.912-34.756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|14 - A|637 }A14 - 637
2X-RAY DIFFRACTION2{ B|24 - B|328 }B24 - 328
3X-RAY DIFFRACTION3{ C|11 - C|20 }C11 - 20

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