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- PDB-6v63: SETD3 WT in Complex with an Actin Peptide with His73 Replaced wit... -

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Basic information

Entry
Database: PDB / ID: 6v63
TitleSETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine
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 / 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 / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton ...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 / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / profilin binding / protein localization to bicellular tight junction / dense body / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / histone H3K36 methyltransferase activity / RSC-type complex / Adherens junctions interactions / regulation of stress fiber assembly / 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 / SWI/SNF complex / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / positive regulation of wound healing / maintenance of blood-brain barrier / myofibril / sarcomere organization / positive regulation of muscle cell differentiation / NuA4 histone acetyltransferase complex / 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 / anatomical structure morphogenesis / RHOBTB2 GTPase cycle / EPHB-mediated forward signaling / phagocytic vesicle / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / cytoskeleton / blood microparticle / hydrolase activity / positive regulation of cell migration / axon / focal adhesion / synapse / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 beta / Actin, cytoplasmic 2 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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
Z: Actin, cytoplasmic 1
B: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,93545
Polymers140,6894
Non-polymers3,24741
Water12,016667
1
Y: Actin, cytoplasmic 1
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,21326
Polymers70,3442
Non-polymers1,86924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint33 kcal/mol
Surface area23490 Å2
MethodPISA
2
Z: Actin, cytoplasmic 1
B: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,72219
Polymers70,3442
Non-polymers1,37717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint17 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.344, 175.795, 66.807
Angle α, β, γ (deg.)90.000, 92.369, 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 1


Mass: 2858.229 Da / Num. of mol.: 2 / Mutation: H73Q / 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: 67486.180 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, 708 molecules

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


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


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 667 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
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: Aug 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→36.71 Å / Num. obs: 84534 / % possible obs: 92.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.21 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.4
Reflection shellResolution: 2.02→2.09 Å / Num. unique obs: 7028 / CC1/2: 0.485

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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: 2.02→36.71 Å / SU ML: 0.2155 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.7352
RfactorNum. reflection% reflection
Rfree0.1988 2009 2.38 %
Rwork0.1661 --
obs0.1669 84474 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.59 Å2
Refinement stepCycle: LAST / Resolution: 2.02→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8047 0 212 667 8926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00398482
X-RAY DIFFRACTIONf_angle_d0.638511438
X-RAY DIFFRACTIONf_chiral_restr0.04341247
X-RAY DIFFRACTIONf_plane_restr0.00421456
X-RAY DIFFRACTIONf_dihedral_angle_d20.35233135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.3251080.28624370X-RAY DIFFRACTION69.12
2.07-2.120.29371450.22935634X-RAY DIFFRACTION89.51
2.12-2.190.23181400.20765957X-RAY DIFFRACTION93.58
2.19-2.260.22441410.19566004X-RAY DIFFRACTION95.01
2.26-2.340.261540.18486056X-RAY DIFFRACTION95.85
2.34-2.430.23031500.18196088X-RAY DIFFRACTION96.58
2.43-2.540.23261470.17596162X-RAY DIFFRACTION97.02
2.54-2.680.24021380.1716104X-RAY DIFFRACTION95.96
2.68-2.840.2011440.17135908X-RAY DIFFRACTION93.35
2.84-3.060.21531390.17265561X-RAY DIFFRACTION87.65
3.06-3.370.18161500.16846274X-RAY DIFFRACTION98.75
3.37-3.860.1761550.14186245X-RAY DIFFRACTION98.57
3.86-4.860.15391470.1326195X-RAY DIFFRACTION97.27
4.86-36.710.15811510.14965907X-RAY DIFFRACTION92.08

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