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- PDB-6wk2: SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 ... -

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Basic information

Entry
Database: PDB / ID: 6wk2
TitleSETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine
Components
  • Actin, cytoplasmic 2
  • Actin-histidine N-methyltransferase
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


basal body patch / protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction ...basal body patch / protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction / morphogenesis of a polarized epithelium / profilin binding / Formation of annular gap junctions / Gap junction degradation / histone H3K36 methyltransferase activity / dense body / Cell-extracellular matrix interactions / regulation of stress fiber assembly / Adherens junctions interactions / histone H3K4 methyltransferase activity / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / sarcomere organization / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / maintenance of blood-brain barrier / positive regulation of wound healing / myofibril / positive regulation of muscle cell differentiation / Recycling pathway of L1 / filamentous actin / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / axonogenesis / actin filament / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / PKMTs methylate histone lysines / platelet aggregation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / 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 / 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 / synapse / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / 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 superfamily / SET domain / SET domain profile. / SET domain ...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 superfamily / SET domain / SET domain profile. / 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-ADENOSYLMETHIONINE / Actin, cytoplasmic 2 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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: Characterization of SETD3 methyltransferase-mediated protein methionine methylation.
Authors: Dai, S. / Holt, M.V. / Horton, J.R. / Woodcock, C.B. / Patel, A. / Zhang, X. / Young, N.L. / Wilkinson, A.W. / Cheng, X.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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 2
A: Actin-histidine N-methyltransferase
C: Actin, cytoplasmic 2
D: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,69315
Polymers140,3774
Non-polymers1,31611
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-24 kcal/mol
Surface area42380 Å2
MethodPISA
2
Y: Actin, cytoplasmic 2
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,02110
Polymers70,1882
Non-polymers8338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-7 kcal/mol
Surface area22500 Å2
MethodPISA
3
C: Actin, cytoplasmic 2
D: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6725
Polymers70,1882
Non-polymers4833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-25 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.342, 175.977, 66.314
Angle α, β, γ (deg.)90.000, 92.578, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein/peptide / Protein , 2 types, 4 molecules YCAD

#1: Protein/peptide Actin, cytoplasmic 2 / / Gamma-actin


Mass: 2861.296 Da / Num. of mol.: 2 / Mutation: H73M / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P63261
#2: Protein Actin-histidine N-methyltransferase / SET domain-containing protein 3 / hSETD3


Mass: 67327.078 Da / Num. of mol.: 2 / Mutation: N255V
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

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Non-polymers , 4 types, 742 molecules

#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 50.91 %
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: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→36.65 Å / Num. obs: 129205 / % possible obs: 94.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 23.65 Å2 / CC1/2: 0.993 / Net I/σ(I): 13.8
Reflection shellResolution: 1.76→1.81 Å / Num. unique obs: 11330 / CC1/2: 0.396

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MBJ

6mbj


Resolution: 1.76→36.65 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.573 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2065 2028 1.57 %
Rwork0.182 127034 -
obs0.1824 129062 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.11 Å2
Refinement stepCycle: LAST / Resolution: 1.76→36.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7913 0 87 731 8731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518242
X-RAY DIFFRACTIONf_angle_d0.781511209
X-RAY DIFFRACTIONf_chiral_restr0.04761249
X-RAY DIFFRACTIONf_plane_restr0.00511435
X-RAY DIFFRACTIONf_dihedral_angle_d15.93184931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.32881330.31417621X-RAY DIFFRACTION79.39
1.8-1.850.34121340.28388541X-RAY DIFFRACTION89.27
1.85-1.90.31441420.26319297X-RAY DIFFRACTION96.32
1.9-1.970.27441510.24079241X-RAY DIFFRACTION96.61
1.97-2.040.28491370.21989319X-RAY DIFFRACTION96.86
2.04-2.120.25541540.1989311X-RAY DIFFRACTION97.21
2.12-2.210.21441510.19189342X-RAY DIFFRACTION96.92
2.21-2.330.2021420.18089232X-RAY DIFFRACTION96.28
2.33-2.480.2211450.18279136X-RAY DIFFRACTION94.96
2.48-2.670.19171350.18318592X-RAY DIFFRACTION89.24
2.67-2.940.17331550.18399438X-RAY DIFFRACTION98.22
2.94-3.360.20611540.17729490X-RAY DIFFRACTION98.22
3.36-4.230.17911440.15179394X-RAY DIFFRACTION97.52
4.23-36.650.17491510.15589080X-RAY DIFFRACTION93.45

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