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- PDB-5fa5: Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide -

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Basic information

Entry
Database: PDB / ID: 5fa5
TitleCrystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide
Components
  • Histone H4
  • Methylosome protein 50
  • Protein arginine N-methyltransferase 5
KeywordsTRANSFERASE/PROTEIN BINDING / Methyl Transferase / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


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 / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone H4R3 methyltransferase activity ...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 / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone H4R3 methyltransferase activity / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of gene expression via chromosomal CpG island methylation / E-box binding / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / negative regulation of megakaryocyte differentiation / regulation of ERK1 and ERK2 cascade / ribonucleoprotein complex binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / methyltransferase activity / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / liver regeneration / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / DNA-templated transcription termination / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / protein polyubiquitination / structural constituent of chromatin / transcription corepressor activity / p53 binding / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / snRNP Assembly / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity
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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Distorted Sandwich / Histone-fold / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / WD40/YVTN repeat-like-containing domain superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / Protein arginine N-methyltransferase 5 / Histone H4 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsSprague, E.R. / McNamara, J.T.
CitationJournal: Science / Year: 2016
Title: Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5.
Authors: Mavrakis, K.J. / McDonald, E.R. / Schlabach, M.R. / Billy, E. / Hoffman, G.R. / deWeck, A. / Ruddy, D.A. / Venkatesan, K. / Yu, J. / McAllister, G. / Stump, M. / deBeaumont, R. / Ho, S. / ...Authors: Mavrakis, K.J. / McDonald, E.R. / Schlabach, M.R. / Billy, E. / Hoffman, G.R. / deWeck, A. / Ruddy, D.A. / Venkatesan, K. / Yu, J. / McAllister, G. / Stump, M. / deBeaumont, R. / Ho, S. / Yue, Y. / Liu, Y. / Yan-Neale, Y. / Yang, G. / Lin, F. / Yin, H. / Gao, H. / Kipp, D.R. / Zhao, S. / McNamara, J.T. / Sprague, E.R. / Zheng, B. / Lin, Y. / Cho, Y.S. / Gu, J. / Crawford, K. / Ciccone, D. / Vitari, A.C. / Lai, A. / Capka, V. / Hurov, K. / Porter, J.A. / Tallarico, J. / Mickanin, C. / Lees, E. / Pagliarini, R. / Keen, N. / Schmelzle, T. / Hofmann, F. / Stegmeier, F. / Sellers, W.R.
History
DepositionDec 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4374
Polymers116,1403
Non-polymers2971
Water3,027168
1
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,75016
Polymers464,56012
Non-polymers1,1894
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area35850 Å2
ΔGint-84 kcal/mol
Surface area136010 Å2
MethodPISA
2
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8758
Polymers232,2806
Non-polymers5952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area14160 Å2
ΔGint-36 kcal/mol
Surface area71770 Å2
MethodPISA
3
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8758
Polymers232,2806
Non-polymers5952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area13950 Å2
ΔGint-35 kcal/mol
Surface area71980 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-15 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.050, 137.850, 178.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 74281.250 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) / Strain (production host): Sf21
References: UniProt: O14744, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Protein Methylosome protein 50 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / p44/Mep50


Mass: 39857.496 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) / Strain (production host): Sf21 / References: UniProt: Q9BQA1
#3: Protein/peptide Histone H4


Mass: 2001.370 Da / Num. of mol.: 1 / Fragment: DNA binding residues 2-21 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#4: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→89.22 Å / Num. obs: 53238 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 56.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Net I/σ(I): 17.2 / Num. measured all: 357014
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.34-2.76.80.5523.1125363184610.9350.228100
4.68-89.226.30.03245.74327569150.9990.01499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.2refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GQB

4gqb


Resolution: 2.34→89.22 Å / Cor.coef. Fo:Fc: 0.9334 / Cor.coef. Fo:Fc free: 0.9044 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.231 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 2625 4.93 %RANDOM
Rwork0.177 ---
obs0.1792 53238 99.83 %-
Displacement parametersBiso max: 161.81 Å2 / Biso mean: 64.79 Å2 / Biso min: 29.52 Å2
Baniso -1Baniso -2Baniso -3
1--21.6318 Å20 Å20 Å2
2--6.7528 Å20 Å2
3---14.879 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.34→89.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7353 0 31 168 7552
Biso mean--57.26 52.08 -
Num. residues----926
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2554SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1090HARMONIC5
X-RAY DIFFRACTIONt_it7569HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion968SEMIHARMONIC5
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_contact8368SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7569HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10307HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion18.79
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3062 172 4.52 %
Rwork0.2215 3630 -
all0.2254 3802 -
obs--99.83 %
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)
10.1342-0.1549-0.01540.9715-0.14181.15650.05950.0282-0.0279-0.1363-0.05270.1480.1659-0.2709-0.0069-0.0455-0.028-0.0523-0.0102-0.0035-0.0212-20.4741-76.7707-19.3068
20.8534-0.09380.18711.5353-0.11462.27480.03860.13050.1425-0.3979-0.09080.1487-0.9067-0.39870.05220.34370.3616-0.0502-0.19620.0784-0.2794-28.3115-27.343-37.3866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A13 - 637
2X-RAY DIFFRACTION2{ B|* }B21 - 328

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