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- PDB-4m38: Crystal structure of Trypanosoma brucei protein arginine methyltr... -

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Basic information

Entry
Database: PDB / ID: 4m38
TitleCrystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with AdoHcy and histone H4 peptide
Components
  • Histone H4
  • Protein arginine N-methyltransferase 7
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / methyltransferase / TRANSFERASE-TRANSFERASE SUBSTRATE complex
Function / homology
Function and homology information


arginine N-methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine N-methylation / peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends ...arginine N-methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine N-methylation / peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Transferases; Transferring one-carbon groups; Methyltransferases / telomere organization / 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 / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / 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) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / nucleosome assembly / HATs acetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Dengue Virus-Host Interactions / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / chromatin organization / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / nucleolus / regulation of DNA-templated transcription / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site ...Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / 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 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H4 / Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, C. / Zhu, Y. / Shi, Y.
CitationJournal: Structure / Year: 2014
Title: Structural determinants for the strict monomethylation activity by trypanosoma brucei protein arginine methyltransferase 7.
Authors: Wang, C. / Zhu, Y. / Caceres, T.B. / Liu, L. / Peng, J. / Wang, J. / Chen, J. / Chen, X. / Zhang, Z. / Zuo, X. / Gong, Q. / Teng, M. / Hevel, J.M. / Wu, J. / Shi, Y.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 7
B: Protein arginine N-methyltransferase 7
E: Histone H4
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9416
Polymers82,1724
Non-polymers7692
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-41 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.696, 72.764, 72.565
Angle α, β, γ (deg.)90.00, 110.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein arginine N-methyltransferase 7 / TbPRMT7


Mass: 38985.469 Da / Num. of mol.: 2 / Fragment: UNP residues 36-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: PRMT7, Tb927.7.5490 / Production host: Escherichia coli (E. coli)
References: UniProt: Q582G4, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide Histone H4


Mass: 2100.501 Da / Num. of mol.: 2 / Fragment: UNP residues 2-22 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 20% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9793 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: NiFILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30812

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23001 1642 5.1 %RANDOM
Rwork0.18779 ---
obs0.18995 30812 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0.13 Å2
2--0.8 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 52 103 5392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195407
X-RAY DIFFRACTIONr_bond_other_d00.025094
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9637343
X-RAY DIFFRACTIONr_angle_other_deg3.562311662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28823.625240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10515884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8381538
X-RAY DIFFRACTIONr_chiral_restr0.0790.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216098
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021253
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3131.8562696
X-RAY DIFFRACTIONr_mcbond_other2.3131.8552695
X-RAY DIFFRACTIONr_mcangle_it2.8112.7633358
X-RAY DIFFRACTIONr_mcangle_other2.812.7643359
X-RAY DIFFRACTIONr_scbond_it3.6222.0482711
X-RAY DIFFRACTIONr_scbond_other3.6212.0472711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4352.9653986
X-RAY DIFFRACTIONr_long_range_B_refined4.70614.7735764
X-RAY DIFFRACTIONr_long_range_B_other4.70414.7715755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 98 -
Rwork0.243 2127 -
obs--92.06 %

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