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- PDB-6wk1: SETD3 in Complex with an Actin Peptide with His73 Replaced with M... -

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Basic information

Entry
Database: PDB / ID: 6wk1
TitleSETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine
Components
  • Actin, cytoplasmic 2
  • Actin-histidine N-methyltransferase
KeywordsTRANSFERASE / 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 / profilin binding ...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 / profilin binding / morphogenesis of a polarized epithelium / protein localization to bicellular tight junction / Formation of annular gap junctions / histone H3K36 methyltransferase activity / dense body / Gap junction degradation / 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 / cell motility / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / 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
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Actin, cytoplasmic 2 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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
Z: Actin, cytoplasmic 2
B: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,64259
Polymers140,4074
Non-polymers4,23655
Water10,827601
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18950 Å2
ΔGint121 kcal/mol
Surface area41420 Å2
2
Y: Actin, cytoplasmic 2
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,87537
Polymers70,2032
Non-polymers2,67235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint43 kcal/mol
Surface area23170 Å2
MethodPISA
3
Z: Actin, cytoplasmic 2
B: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,76722
Polymers70,2032
Non-polymers1,56420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint16 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.388, 175.531, 66.654
Angle α, β, γ (deg.)90.000, 92.359, 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 YZAB

#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: 67342.047 Da / Num. of mol.: 2
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 , 5 types, 656 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 51.07 %
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: 1.89→36 Å / Num. obs: 102262 / % possible obs: 93.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 0.986 / Net I/σ(I): 10.2
Reflection shellResolution: 1.89→1.96 Å / Num. unique obs: 8146 / CC1/2: 0.526

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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: 1.89→36 Å / SU ML: 0.2308 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1001 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2281 2001 1.96 %
Rwork0.1947 100198 -
obs0.1954 102199 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.19 Å2
Refinement stepCycle: LAST / Resolution: 1.89→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 276 601 8900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00478501
X-RAY DIFFRACTIONf_angle_d0.744911439
X-RAY DIFFRACTIONf_chiral_restr0.04551244
X-RAY DIFFRACTIONf_plane_restr0.00491453
X-RAY DIFFRACTIONf_dihedral_angle_d16.82375082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.37521080.3095249X-RAY DIFFRACTION68.6
1.94-1.990.31581330.28136274X-RAY DIFFRACTION81.79
1.99-2.050.28151190.26126376X-RAY DIFFRACTION83.66
2.05-2.120.27041490.24157292X-RAY DIFFRACTION94.91
2.12-2.190.2581550.21657487X-RAY DIFFRACTION98.05
2.19-2.280.2471460.20297548X-RAY DIFFRACTION98.33
2.28-2.390.26011510.20557554X-RAY DIFFRACTION98.18
2.39-2.510.26141500.20757555X-RAY DIFFRACTION98.28
2.51-2.670.25371480.20537585X-RAY DIFFRACTION99.14
2.67-2.880.23531450.19817272X-RAY DIFFRACTION94.44
2.88-3.170.22961420.19647315X-RAY DIFFRACTION95.27
3.17-3.620.2211570.1827611X-RAY DIFFRACTION99.69
3.62-4.560.17551530.16057654X-RAY DIFFRACTION99.34
4.56-360.18411450.16717426X-RAY DIFFRACTION95.42

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