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- PDB-7boc: Crystal structure of the PRMT5 TIM barrel domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7boc
TitleCrystal structure of the PRMT5 TIM barrel domain in complex with RioK1 peptide
Components
  • Protein arginine N-methyltransferase 5
  • peptide
KeywordsTRANSFERASE / TIM barrel / Methyltransferase / Histones / Chromatin-regulator / protein-peptide interaction
Function / homology
Function and homology information


positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / histone H2AQ104 methyltransferase activity / endothelial cell activation / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase complex / negative regulation of gene expression via chromosomal CpG island methylation / histone methyltransferase activity / E-box binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / circadian regulation of gene expression / DNA-templated transcription termination / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / transcription corepressor activity / p53 binding / snRNP Assembly / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsKrzyzanowski, A. / t Hart, P. / Waldmann, H. / Gasper, R.
CitationJournal: Chembiochem / Year: 2021
Title: Biochemical Investigation of the Interaction of pICln, RioK1 and COPR5 with the PRMT5-MEP50 Complex.
Authors: Krzyzanowski, A. / Gasper, R. / Adihou, H. / t Hart, P. / Waldmann, H.
History
DepositionJan 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: peptide


Theoretical massNumber of molelcules
Total (without water)34,8742
Polymers34,8742
Non-polymers00
Water00
1
A: Protein arginine N-methyltransferase 5
B: peptide

A: Protein arginine N-methyltransferase 5
B: peptide


Theoretical massNumber of molelcules
Total (without water)69,7484
Polymers69,7484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4200 Å2
ΔGint-28 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.630, 96.630, 112.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 33278.160 Da / Num. of mol.: 1 / Fragment: TIM barrel domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Plasmid: pOPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon+RIPL
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein/peptide peptide


Mass: 1595.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M NaAcetate, 30% w/v PEG400, 0.2M CaAcetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999859 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999859 Å / Relative weight: 1
ReflectionResolution: 2.55→48.31 Å / Num. obs: 20297 / % possible obs: 99.9 % / Redundancy: 20.164 % / Biso Wilson estimate: 83.077 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.191 / Rrim(I) all: 0.196 / Χ2: 0.766 / Net I/σ(I): 12.05 / Num. measured all: 409271 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.6221.1444.2891.2731631149814960.7874.39599.9
2.62-2.6920.9813.7481.5530066143414330.9293.84299.9
2.69-2.7720.8283.221.8229326140914080.8493.399.9
2.77-2.8520.7052.5212.3527972135413510.9172.58499.8
2.85-2.9420.3811.8783.3226903132013200.9411.926100
2.94-3.0520.0551.434.3825690128512810.9491.46799.7
3.05-3.1619.3781.0525.6523971123912370.9761.08199.8
3.16-3.2917.3530.7287.1820477118311800.9830.7599.7
3.29-3.4420.550.69.3623633115111500.9970.61699.9
3.44-3.6121.4850.39612.9323633110011000.9970.406100
3.61-3.821.4010.29215.7522300104210420.9980.299100
3.8-4.0321.1950.20219.5921195100010000.9980.206100
4.03-4.3120.9550.14623.32195099319310.9980.149100
4.31-4.6620.2990.12426.03180058878870.9970.127100
4.66-5.119.7580.11626.97160838148140.9960.119100
5.1-5.718.8980.11327.38139287377370.9970.116100
5.7-6.5816.1990.10826.6104816476470.9970.112100
6.58-8.0620.0020.09432.48114015705700.9980.096100
8.06-11.419.4590.07536.7286984474470.9990.077100
11.4-48.3116.4250.06634.4843692692660.9980.06898.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.05 Å83.64 Å
Translation4.05 Å83.64 Å

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Processing

Software
NameVersionClassification
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
XSCALEVERSION Jan 31, 2020 BUILT=20200417data scaling
PHASER2.8.3phasing
PHENIX1.18-3855refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4x60

4x60


Resolution: 2.55→48.31 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1011 5 %
Rwork0.2253 19210 -
obs0.2266 20221 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.73 Å2 / Biso mean: 92.7794 Å2 / Biso min: 49.79 Å2
Refinement stepCycle: final / Resolution: 2.55→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 0 1844
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.680.34381420.34252689283199
2.68-2.850.37881400.32462689282999
2.85-3.070.36641430.29792701284499
3.07-3.380.31361430.279327202863100
3.38-3.870.26731450.238227532898100
3.87-4.870.21341460.195727622908100
4.88-48.310.21551520.194828963048100
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)
12.2723-0.269-0.6782-0.0068-0.15034.5361-0.148-0.2117-0.19560.05510.04740.38280.25230.16490.35950.56940.0474-0.0360.6964-0.08470.5419-32.817837.015317.6137
24.43841.6530.25327.87390.61594.33290.0731-0.5704-0.44450.61980.089-0.22320.3550.5699-0.0720.5859-0.04220.08450.73330.06830.4527-37.482831.132728.955
39.52091.3929-0.68986.05-1.83545.9257-0.7858-0.60780.63580.56250.67680.06330.01650.60120.17550.47240.08070.00780.7118-0.03110.4644-42.692936.819727.4767
42.6132-1.313-2.62831.03111.38442.9915-0.43320.6697-0.935-0.7252-0.08060.00890.95710.05550.36141.0965-0.2109-0.04490.905-0.07280.5562-47.134321.70288.1471
57.5835-0.7477-3.32223.7926-1.60839.3836-0.12950.3338-0.04870.6194-0.63330.7290.6757-1.65820.44640.4524-0.07950.08360.6414-0.0390.659-51.401930.514517.656
65.91020.6122-3.12863.89190.11745.8768-0.02710.22290.0007-0.35330.0897-0.1039-0.4450.01610.1090.6181-0.0467-0.07320.50990.02360.4031-36.926636.33294.0966
71.5491-0.7406-0.29611.4304-1.39062.623-0.13511.29230.0528-0.67550.3497-0.1815-0.38950.9526-0.39911.1178-0.22940.13071.0664-0.15970.6412-25.879638.1626-9.5446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 96 )A41 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 131 )A97 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 156 )A132 - 156
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 183 )A157 - 183
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 195 )A184 - 195
6X-RAY DIFFRACTION6chain 'A' and (resid 196 through 290 )A196 - 290
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 14 )B1 - 14

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