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- PDB-6sqk: Crystal structure of mouse PRMT6 with modified H7-4 peptide -

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Basic information

Entry
Database: PDB / ID: 6sqk
TitleCrystal structure of mouse PRMT6 with modified H7-4 peptide
Components
  • H4-7
  • Protein arginine N-methyltransferase 6
KeywordsTRANSFERASE / SAM binding domain / arginine methylation
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / : / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / : / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / histone binding / methylation / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain 25 / Methyltransferase domain / 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 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBonnefond, L. / Cavarelli, J.
CitationJournal: To Be Published
Title: Crystal structure of mouse PRMT6 in complex with inhibitors
Authors: Bonnefond, L. / Cavarelli, J.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
B: Protein arginine N-methyltransferase 6
D: H4-7
E: H4-7


Theoretical massNumber of molelcules
Total (without water)85,9474
Polymers85,9474
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-42 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.632, 142.829, 41.701
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 Protein arginine N-methyltransferase 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 42077.523 Da / Num. of mol.: 2 / Mutation: F315L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt6, Hrmt1l6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6NZB1, type I protein arginine methyltransferase
#2: Protein/peptide H4-7


Mass: 895.945 Da / Num. of mol.: 2 / Mutation: R4(URG) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3,350 20%, Mg(CH3COO)2 200 mM, HEPES-NaOH pH 7.0 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.4→47.61 Å / Num. obs: 140415 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.039 / Rrim(I) all: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 12.7 % / Rmerge(I) obs: 2.523 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13708 / CC1/2: 0.395 / Rpim(I) all: 0.734 / Rrim(I) all: 2.629 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.16_3546refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c03

4c03


Resolution: 1.4→45.629 Å / Cross valid method: THROUGHOUT / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.2128 7012 5 %
Rwork0.19 --
obs0.1911 140271 99.95 %
Displacement parametersBiso max: 100.21 Å2 / Biso mean: 27.3722 Å2 / Biso min: 11.93 Å2
Refinement stepCycle: final / Resolution: 1.4→45.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 72 215 5656
Biso mean--33.99 29.66 -
Num. residues----676
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)
10.89-0.42080.29080.3265-0.05690.1517-0.02090.05480.05910.02060.018-0.04180.00250.01810.00180.14520.0002-0.00690.19930.00680.201512.931249.53028.5021
21.0194-0.23420.00260.6797-0.01450.2265-0.02650.0689-0.09420.01830.02320.0868-0.0385-0.0003-0.00140.113-0.00660.0090.1539-0.00130.141717.806913.504613.4516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 42 through 378)B42 - 378
2X-RAY DIFFRACTION2(chain 'A' and resid 42 through 378)A42 - 378

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