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- PDB-6ox4: A SETD3 Mutant (N255A) in Complex with an Actin Peptide -

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Basic information

Entry
Database: PDB / ID: 6ox4
TitleA SETD3 Mutant (N255A) in Complex with an Actin Peptide
Components
  • Actin Peptide
  • Actin-histidine N-methyltransferase
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / histone H3K36 methyltransferase activity ...peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / histone H3K36 methyltransferase activity / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBAF complex / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / dense body / postsynaptic actin cytoskeleton / Tat protein binding / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / histone H3K4 methyltransferase activity / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / positive regulation of muscle cell differentiation / apical junction complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / nitric-oxide synthase binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / kinesin binding / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / adherens junction / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / kinetochore / Regulation of actin dynamics for phagocytic cup formation / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / platelet aggregation / VEGFA-VEGFR2 Pathway / tau protein binding / Schaffer collateral - CA1 synapse / nuclear matrix / cytoplasmic ribonucleoprotein granule / 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
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 superfamily / SET domain profile. ...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 superfamily / 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 1 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsHorton, J.R. / Dai, S. / 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
Citation
Journal: Nat Commun / Year: 2019
Title: Structural basis for the target specificity of actin histidine methyltransferase SETD3.
Authors: Dai, S. / Horton, J.R. / Woodcock, C.B. / Wilkinson, A.W. / Zhang, X. / Gozani, O. / Cheng, X.
#1: Journal: Nature / Year: 2019
Title: SETD3 is an actin histidine methyltransferase that prevents primary dystocia.
Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / ...Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / Mak, J. / Cowan, T. / Elias, J.E. / Nagamine, C.M. / Spudich, J.A. / Cheng, X. / Carette, J.E. / Gozani, O.
History
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 Peptide
A: Actin-histidine N-methyltransferase
Z: Actin Peptide
B: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,14643
Polymers138,9974
Non-polymers3,14939
Water7,819434
1
Y: Actin Peptide
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,33225
Polymers69,4982
Non-polymers1,83423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Z: Actin Peptide
B: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,81418
Polymers69,4982
Non-polymers1,31516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.393, 177.039, 65.913
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

#1: Protein/peptide Actin Peptide / Beta-actin


Mass: 1788.008 Da / Num. of mol.: 2 / Fragment: residues 66-80 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709
#2: Protein Actin-histidine N-methyltransferase / SET domain-containing protein 3 / hSETD3


Mass: 67710.484 Da / Num. of mol.: 2 / Mutation: N255A
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, 473 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6O2
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
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: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→36.733 Å / Num. obs: 58449 / % possible obs: 95.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.112 / Net I/σ(I): 8.8
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4402 / CC1/2: 0.409 / Rpim(I) all: 0.437 / % possible all: 75

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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: 2.294→36.733 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2364 1999 3.42 %
Rwork0.1879 --
obs0.1896 58365 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.294→36.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7907 0 206 434 8547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038371
X-RAY DIFFRACTIONf_angle_d0.5311316
X-RAY DIFFRACTIONf_dihedral_angle_d15.9674966
X-RAY DIFFRACTIONf_chiral_restr0.0381241
X-RAY DIFFRACTIONf_plane_restr0.0041440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2943-2.35170.3045920.25042724X-RAY DIFFRACTION64
2.3517-2.41530.32041280.27073418X-RAY DIFFRACTION81
2.4153-2.48630.35231220.26453782X-RAY DIFFRACTION90
2.4863-2.56660.33851530.25054116X-RAY DIFFRACTION97
2.5666-2.65830.29791560.24084219X-RAY DIFFRACTION99
2.6583-2.76470.29081490.22474261X-RAY DIFFRACTION100
2.7647-2.89040.29511420.20494221X-RAY DIFFRACTION100
2.8904-3.04280.27411580.20624221X-RAY DIFFRACTION99
3.0428-3.23330.24041450.19584211X-RAY DIFFRACTION100
3.2333-3.48280.23611580.18444218X-RAY DIFFRACTION99
3.4828-3.83290.18141570.15584232X-RAY DIFFRACTION100
3.8329-4.38680.20721500.1544256X-RAY DIFFRACTION100
4.3868-5.52380.19081430.16524260X-RAY DIFFRACTION99
5.5238-36.73820.20871460.16854227X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00190.000100.0058-0.0060.00520.0224-0.02310.00610.0068-0.0195-0.01320.07460-00.27210.039-0.0180.3757-0.07710.505-1.6438-7.762116.8545
20.2057-0.0473-0.09630.3350.0020.2895-0.01960.125-0.3681-0.02190.01180.2150.0534-0.0540.1050.09560.0068-0.03450.1781-0.12710.14595.7824-0.17939.1872
30.1227-0.05550.06280.066-0.05740.0790.0313-0.0351-0.0460.0716-0.05510.02090.01580.0022-00.238-0.02650.03290.1903-0.01080.179112.3152-20.131738.4348
40.0004-0.00020.00220.0038-0.00180.0024-0.0073-0.00430.00610.01910.0082-0.013-0.02620.02500.32230.00140.01070.35030.11170.586928.324438.90914.5915
50.1831-0.05190.0750.18360.08660.27110.09060.06150.2727-0.0976-0.0716-0.1821-0.04820.00940.02510.17140.05520.02450.1950.07410.262521.377130.31598.2167
60.06760.0163-0.05810.03470.01830.10940.0569-0.0087-0.00640.1176-0.00040.0405-0.00030.035200.2596-0.0123-0.02020.2004-0.01120.242814.774451.595236.5972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Y' and (resid 66 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 334 )
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 501 )
4X-RAY DIFFRACTION4chain 'Z' and (resid 66 through 80 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 334 )
6X-RAY DIFFRACTION6chain 'B' and (resid 335 through 501 )

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