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- PDB-6v62: SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptid... -

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Basic information

Entry
Database: PDB / ID: 6v62
TitleSETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine
Components
  • Actin, cytoplasmic 1
  • Actin-histidine N-methyltransferase
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


basal body patch / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / profilin binding / histone H3K36 methyltransferase activity / protein localization to bicellular tight junction ...basal body patch / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / profilin binding / histone H3K36 methyltransferase activity / protein localization to bicellular tight junction / regulation of transepithelial transport / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / Cell-extracellular matrix interactions / dense body / regulation of stress fiber assembly / histone H3K4 methyltransferase activity / Adherens junctions interactions / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / sarcomere organization / Sensory processing of sound by inner hair cells of the cochlea / regulation of focal adhesion assembly / positive regulation of muscle cell differentiation / positive regulation of wound healing / apical junction complex / maintenance of blood-brain barrier / filamentous actin / myofibril / NuA4 histone acetyltransferase complex / Recycling pathway of L1 / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / axonogenesis / calyx of Held / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / PKMTs methylate histone lysines / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / VEGFA-VEGFR2 Pathway / platelet aggregation / Schaffer collateral - CA1 synapse / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / actin cytoskeleton / Clathrin-mediated endocytosis / actin binding / angiogenesis / blood microparticle / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / cytoskeleton / hydrolase activity / positive regulation of cell migration / axon / focal adhesion / ubiquitin protein ligase binding / synapse / positive regulation of gene expression / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET domain / SET domain profile. / SET domain superfamily ...Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET domain / SET domain profile. / SET domain superfamily / SET domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Actin beta / Actin, cytoplasmic 2 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsDai, S. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation.
Authors: Dai, S. / Horton, J.R. / Wilkinson, A.W. / Gozani, O. / Zhang, X. / Cheng, X.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Actin, cytoplasmic 1
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9588
Polymers70,2632
Non-polymers6956
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint3 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.654, 116.752, 174.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein/peptide Actin, cytoplasmic 1


Mass: 2859.280 Da / Num. of mol.: 1 / Mutation: H73K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JUM1, UniProt: P63261*PLUS
#2: Protein Actin-histidine N-methyltransferase / SET domain-containing protein 3 / hSETD3


Mass: 67404.117 Da / Num. of mol.: 1 / Mutation: N255F, W273A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86TU7, protein-histidine N-methyltransferase
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 24952 / % possible obs: 96 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.61 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.2 % / Num. unique obs: 2284 / CC1/2: 0.529 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MBJ

6mbj


Resolution: 2.36→39.49 Å / SU ML: 0.3271 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.0706
RfactorNum. reflection% reflection
Rfree0.2524 1235 4.99 %
Rwork0.208 --
obs0.2102 24735 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.58 Å2
Refinement stepCycle: LAST / Resolution: 2.36→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 46 187 4197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594120
X-RAY DIFFRACTIONf_angle_d0.52415591
X-RAY DIFFRACTIONf_chiral_restr0.0419620
X-RAY DIFFRACTIONf_plane_restr0.0034717
X-RAY DIFFRACTIONf_dihedral_angle_d18.27441502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.450.32641170.26832238X-RAY DIFFRACTION83.22
2.45-2.560.3071240.26432361X-RAY DIFFRACTION87.47
2.56-2.70.32411310.2652499X-RAY DIFFRACTION91.86
2.7-2.870.3431380.25312632X-RAY DIFFRACTION96.21
2.87-3.090.26721420.23912686X-RAY DIFFRACTION98.95
3.09-3.40.29891430.22832725X-RAY DIFFRACTION99.93
3.4-3.890.22651450.18582753X-RAY DIFFRACTION99.45
3.89-4.90.18241440.16552744X-RAY DIFFRACTION98.9
4.9-39.490.23081510.18542862X-RAY DIFFRACTION98.79

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