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- PDB-6mbl: SETD3, a Histidine Methyltransferase, in Complex with an Actin Pe... -

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Basic information

Entry
Database: PDB / ID: 6mbl
TitleSETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second P212121 Crystal Form
Components
  • Actin Peptide
  • Histone-lysine N-methyltransferase setd3
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 / nBAF complex ...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 / nBAF complex / brahma complex / histone H3K36 methyltransferase activity / 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 / protein localization to adherens junction / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / dense body / Tat protein binding / postsynaptic actin cytoskeleton / 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 / maintenance of blood-brain barrier / transporter regulator activity / 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 / negative regulation of cell differentiation / kinesin binding / 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 / VEGFA-VEGFR2 Pathway / platelet aggregation / Schaffer collateral - CA1 synapse / tau protein binding / 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
set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding 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 / : ...set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding 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 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
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: 2.197 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
CitationJournal: 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
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Assembly

Deposited unit
Y: Actin Peptide
A: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54713
Polymers69,5422
Non-polymers1,00511
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint12 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.557, 92.830, 111.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 1788.008 Da / Num. of mol.: 1 / Fragment: residues 66-80 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709
#2: Protein Histone-lysine N-methyltransferase setd3 / SET domain-containing protein 3


Mass: 67753.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q86TU7, histone-lysine N-methyltransferase
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→48.3 Å / Num. obs: 30434 / % possible obs: 99.5 % / Redundancy: 10.6 % / Rpim(I) all: 0.066 / Net I/σ(I): 14.1
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2920 / CC1/2: 0.402 / Rpim(I) all: 0.548 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3smt

3smt


Resolution: 2.197→48.299 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1520 5.01 %
Rwork0.1824 --
obs0.1846 30334 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→48.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 66 139 4199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044209
X-RAY DIFFRACTIONf_angle_d0.6835698
X-RAY DIFFRACTIONf_dihedral_angle_d16.8792549
X-RAY DIFFRACTIONf_chiral_restr0.042622
X-RAY DIFFRACTIONf_plane_restr0.004729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1967-2.26760.34081250.2772341X-RAY DIFFRACTION90
2.2676-2.34860.30211360.24572583X-RAY DIFFRACTION99
2.3486-2.44270.29451370.22792612X-RAY DIFFRACTION100
2.4427-2.55380.25941380.20722607X-RAY DIFFRACTION100
2.5538-2.68850.25791380.20562623X-RAY DIFFRACTION100
2.6885-2.85690.27031380.19362623X-RAY DIFFRACTION100
2.8569-3.07740.2431380.19082615X-RAY DIFFRACTION100
3.0774-3.3870.24491390.1932650X-RAY DIFFRACTION99
3.387-3.8770.21961410.16562660X-RAY DIFFRACTION100
3.877-4.88380.16511410.14212698X-RAY DIFFRACTION100
4.8838-48.31060.19981490.17112802X-RAY DIFFRACTION99
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)
16.20871.6804-2.20846.02590.34558.7552-0.0355-0.57310.11550.2571-0.0655-0.02390.20940.36260.18670.2042-0.0065-0.02390.1967-0.02920.2562-2.357214.503830.1804
24.2512.41652.07725.58032.35655.34540.11240.2352-0.56970.00590.1106-0.52210.2630.4788-0.30790.17190.0625-0.00880.31520.03860.467925.22522.484124.245
34.1433-1.7492-0.28713.52290.42461.75160.2590.90060.1912-0.7717-0.30350.4665-0.3089-0.19820.04550.40170.0639-0.12330.52420.04440.3491-4.819718.942110.0566
44.61770.93410.95252.66090.25541.69780.07390.3536-0.4628-0.1636-0.04850.04750.20670.0217-0.02050.19240.04020.02440.2068-0.03970.24398.56035.287321.282
54.7367-0.6112-0.30931.83990.5992.5470.00320.22360.0405-0.0534-0.06540.4386-0.0476-0.16360.07530.18710.0025-0.04820.20240.01110.2741-0.694216.17422.3893
64.22511.5302-4.22511.6782-2.16226.3226-0.0957-0.72020.00310.32330.0689-0.04350.12470.44660.06250.43060.07740.02530.3416-0.03210.26538.275324.734557.0144
71.9330.2109-0.77392.1187-0.39742.92660.2724-0.40110.57660.5222-0.05610.1435-0.92390.313-0.2760.5107-0.10490.06010.3149-0.05390.483515.636535.234243.3387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Y' and (resid 66 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 126 )
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 225 )
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 334 )
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 408 )
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 500 )

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