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- PDB-4gqb: Crystal Structure of the human PRMT5:MEP50 Complex -

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Basic information

Entry
Database: PDB / ID: 4gqb
TitleCrystal Structure of the human PRMT5:MEP50 Complex
Components
  • Histone H4 peptide
  • Methylosome protein 50
  • Protein arginine N-methyltransferase 5
KeywordsTRANSFERASE/PROTEIN BINDING / TIM BARREL / BETA-PROPELLER / METHYLTRANSFERASE / METHYLATION / 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 / : / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / liver regeneration / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Regulation of TP53 Activity through Methylation / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / 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 / transcription corepressor activity / structural constituent of chromatin / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / snRNP Assembly / Oxidative Stress Induced Senescence / ubiquitin-dependent protein catabolic process / 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
Chem-0XU / Protein arginine N-methyltransferase 5 / Histone H4 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsAntonysamy, S. / Bonday, Z. / Campbell, R. / Doyle, B. / Druzina, Z. / Gheyi, T. / Han, B. / Jungheim, L.N. / Qian, Y. / Rauch, C. ...Antonysamy, S. / Bonday, Z. / Campbell, R. / Doyle, B. / Druzina, Z. / Gheyi, T. / Han, B. / Jungheim, L.N. / Qian, Y. / Rauch, C. / Russell, M. / Sauder, J.M. / Wasserman, S.R. / Weichert, K. / Willard, F.S. / Zhang, A. / Emtage, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of the human PRMT5:MEP50 complex.
Authors: Antonysamy, S. / Bonday, Z. / Campbell, R.M. / Doyle, B. / Druzina, Z. / Gheyi, T. / Han, B. / Jungheim, L.N. / Qian, Y. / Rauch, C. / Russell, M. / Sauder, J.M. / Wasserman, S.R. / ...Authors: Antonysamy, S. / Bonday, Z. / Campbell, R.M. / Doyle, B. / Druzina, Z. / Gheyi, T. / Han, B. / Jungheim, L.N. / Qian, Y. / Rauch, C. / Russell, M. / Sauder, J.M. / Wasserman, S.R. / Weichert, K. / Willard, F.S. / Zhang, A. / Emtage, S.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1564
Polymers111,7773
Non-polymers3791
Water5,405300
1
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Histone H4 peptide
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)448,62416
Polymers447,10612
Non-polymers1,5174
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
Buried area35900 Å2
ΔGint-91 kcal/mol
Surface area134440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.981, 138.762, 178.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / SKB1 homolog / SKB1Hs / Protein arginine N-methyltransferase 5 / N-terminally processed


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, 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: 36883.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, HKMT1069, Nbla10071 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BQA1
#3: Protein/peptide Histone H4 peptide


Mass: 2126.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#4: Chemical ChemComp-0XU / (2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid


Mass: 379.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N7O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-30% PEG3350, 100-250 mM ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. obs: 77934 / Biso Wilson estimate: 36.52 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.1 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.06→19.71 Å / Cor.coef. Fo:Fc: 0.9566 / Cor.coef. Fo:Fc free: 0.9417 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 3999 5.13 %RANDOM
Rwork0.1884 ---
obs0.1901 77934 99.65 %-
Displacement parametersBiso mean: 59.24 Å2
Baniso -1Baniso -2Baniso -3
1--9.6516 Å20 Å20 Å2
2--3.6278 Å20 Å2
3---6.0238 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.06→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7321 0 27 300 7648
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017551HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1410297HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1098HARMONIC5
X-RAY DIFFRACTIONt_it7551HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion17.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion971SEMIHARMONIC5
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_contact8536SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 301 5.23 %
Rwork0.223 5453 -
all0.2247 5754 -
obs--99.65 %
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)
10.5527-0.2930.06931.3303-0.12351.29650.0380.00130.0492-0.1065-0.0284-0.19540.09790.3294-0.00950.47260.05010.0474-0.1748-0.0282-0.2482-25.7662-84.679-25.3702
20.62830.22160.26761.06850.5011.5334-0.01520.02460.0867-0.1225-0.0039-0.1006-0.43060.15630.0190.5883-0.06330.0135-0.24060.0123-0.2613-34.7619-42.0262-14.3584
30.6155-0.0777-0.34491.4142-0.11041.9201-0.02410.09-0.1016-0.2817-0.0329-0.11440.66770.27930.0570.67310.20160.0691-0.2757-0.0602-0.3476-23.1356-110.594-37.5334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 291
2X-RAY DIFFRACTION2A330 - 637
3X-RAY DIFFRACTION3B21 - 329

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