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

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Basic information

Entry
Database: PDB / ID: 6mbj
TitleSETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 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 / 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 / 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 / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / 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 / maintenance of blood-brain barrier / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / cytoskeleton organization / EPHB-mediated forward signaling / 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 / Regulation of actin dynamics for phagocytic cup formation / kinetochore / 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 profile. / SET domain superfamily / 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
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: 1.78 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,41946
Polymers139,0834
Non-polymers3,33642
Water11,007611
1
Y: Actin Peptide
A: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,50027
Polymers69,5422
Non-polymers1,95825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Z: Actin Peptide
B: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,91919
Polymers69,5422
Non-polymers1,37717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.351, 176.168, 66.577
Angle α, β, γ (deg.)90.00, 92.86, 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 / 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.: 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, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 653 molecules

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


Mass: 62.068 Da / Num. of mol.: 35 / 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.: 611 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Temp details: Room temp

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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 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→39.07 Å / Num. obs: 124387 / % possible obs: 94.5 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.041 / Net I/σ(I): 14.5
Reflection shellResolution: 1.78→1.85 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 10380 / CC1/2: 0.463 / Rpim(I) all: 0.436 / % possible all: 78.9

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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: 1.78→39.068 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1992 1.61 %
Rwork0.1994 --
obs0.1998 123744 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→39.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7972 0 218 611 8801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038464
X-RAY DIFFRACTIONf_angle_d0.56411422
X-RAY DIFFRACTIONf_dihedral_angle_d21.8873137
X-RAY DIFFRACTIONf_chiral_restr0.0391240
X-RAY DIFFRACTIONf_plane_restr0.0041457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7798-1.82430.40961060.37076453X-RAY DIFFRACTION69
1.8243-1.87360.37791260.32587577X-RAY DIFFRACTION82
1.8736-1.92870.29291310.28738118X-RAY DIFFRACTION88
1.9287-1.9910.29191380.26698448X-RAY DIFFRACTION91
1.991-2.06220.29041410.24998641X-RAY DIFFRACTION93
2.0622-2.14470.25711450.24498842X-RAY DIFFRACTION95
2.1447-2.24230.24831460.23098913X-RAY DIFFRACTION96
2.2423-2.36050.23751490.21039126X-RAY DIFFRACTION98
2.3605-2.50840.21211510.20799211X-RAY DIFFRACTION99
2.5084-2.7020.25261510.20829229X-RAY DIFFRACTION99
2.702-2.97390.22311490.19789202X-RAY DIFFRACTION99
2.9739-3.4040.2311530.18999295X-RAY DIFFRACTION100
3.404-4.28780.17071520.15679314X-RAY DIFFRACTION100
4.2878-39.07710.18671540.16519383X-RAY DIFFRACTION100
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)
17.83792.73371.55326.0489-1.58012.0013-0.35990.0464-0.80790.16450.11840.39770.8824-0.22260.23960.2704-0.0480.02820.1678-0.00940.4346-1.8443-8.157817.3392
23.686-0.6804-0.04391.45360.02343.11350.12190.5298-0.4083-0.2903-0.1146-0.19610.28150.359-0.00530.2554-0.03780.02270.217-0.09170.298316.4862-0.04463.4164
31.8761-0.4473-0.45111.37970.13951.36990.01970.2118-0.2206-0.1277-0.090.22550.1256-0.18680.06770.1389-0.0114-0.01140.1508-0.0370.26442.5837-0.352411.507
42.75883.9606-1.34077.744-2.89961.46310.0342-0.0226-0.0680.12080.01720.07350.0637-0.043-0.05140.18320.01080.01110.1844-0.03240.181511.5139-22.371137.5091
52.65283.5445-3.57519.4-8.12397.7960.1365-0.29320.01930.7469-0.259-0.0971-0.41790.14390.11910.2562-0.01630.02630.2079-0.08540.228613.552-12.394843.2343
65.89534.50191.03864.94830.7257.2299-0.4005-0.11210.74280.02550.0533-0.3064-0.79250.14980.34580.3167-0.04380.10690.17780.02270.681528.403238.930614.9231
73.9353-1.6309-2.02739.29865.18316.2056-0.01130.56010.5027-1.1035-0.26160.4064-1.1731-0.38590.27360.40830.1058-0.0850.41890.13010.50110.733237.49761.3216
81.9061-0.67910.2141.5401-0.02631.20990.13810.24170.4295-0.2693-0.1037-0.2732-0.13690.1306-0.03020.19080.0110.06110.17680.05480.408724.112529.06899.4488
92.08783.09040.91686.94052.52821.41810.1455-0.16940.020.461-0.0042-0.02860.04680.0783-0.14660.21440.02170.00320.1961-0.00220.318614.562751.483936.686
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 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 457 )
5X-RAY DIFFRACTION5chain 'A' and (resid 458 through 500 )
6X-RAY DIFFRACTION6chain 'Z' and (resid 66 through 80 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 62 )
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 334 )
9X-RAY DIFFRACTION9chain 'B' and (resid 335 through 501 )

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