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- PDB-6ox1: SETD3 in Complex with an Actin Peptide with Target Histidine Part... -

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Basic information

Entry
Database: PDB / ID: 6ox1
TitleSETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated
Components
  • Actin, cytoplasmic 1
  • Histone-lysine N-methyltransferase setd3
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / brahma complex / nBAF complex / GBAF complex / dense body / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / histone H3K36 methyltransferase activity / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RHOF GTPase cycle / RSC-type complex / Adherens junctions interactions / tight junction / histone H3K4 methyltransferase activity / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / positive regulation of muscle cell differentiation / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / PKMTs methylate histone lysines / Regulation of actin dynamics for phagocytic cup formation / kinetochore / platelet aggregation / nuclear matrix / VEGFA-VEGFR2 Pathway / 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 / UCH proteinases / nucleosome / Signaling by BRAF and RAF1 fusions
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
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: 1.949 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 1.2Jan 29, 2020Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Oct 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: Histone-lysine N-methyltransferase setd3
B: Histone-lysine N-methyltransferase setd3
Z: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,33529
Polymers139,1094
Non-polymers2,22625
Water13,475748
1
Y: Actin, cytoplasmic 1
A: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,96219
Polymers69,5552
Non-polymers1,40817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint22 kcal/mol
Surface area22830 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase setd3
Z: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,37310
Polymers69,5552
Non-polymers8198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint2 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.308, 175.865, 66.967
Angle α, β, γ (deg.)90.00, 92.38, 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, cytoplasmic 1 / Beta-actin


Mass: 1801.027 Da / Num. of mol.: 2 / 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.: 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 , 4 types, 773 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.12 %
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 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→31.27 Å / Num. obs: 99091 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.083 / Net I/σ(I): 11.7
Reflection shellResolution: 1.949→2.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 9993 / CC1/2: 0.461 / Rpim(I) all: 0.499 / % possible all: 99.4

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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: 1.949→31.268 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 1993 2.02 %
Rwork0.1701 --
obs0.1708 98908 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→31.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8017 0 146 748 8911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068497
X-RAY DIFFRACTIONf_angle_d0.74311512
X-RAY DIFFRACTIONf_dihedral_angle_d16.3055086
X-RAY DIFFRACTIONf_chiral_restr0.0491253
X-RAY DIFFRACTIONf_plane_restr0.0051473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9492-1.99790.29731370.23236611X-RAY DIFFRACTION94
1.9979-2.0520.27171440.21477019X-RAY DIFFRACTION99
2.052-2.11230.24271450.2066996X-RAY DIFFRACTION99
2.1123-2.18050.25611440.19296980X-RAY DIFFRACTION99
2.1805-2.25840.20451440.18516977X-RAY DIFFRACTION98
2.2584-2.34880.2291420.18296896X-RAY DIFFRACTION98
2.3488-2.45570.2361370.18666661X-RAY DIFFRACTION94
2.4557-2.58510.19141440.17816944X-RAY DIFFRACTION98
2.5851-2.74690.21981450.1767067X-RAY DIFFRACTION100
2.7469-2.95890.23491450.17157037X-RAY DIFFRACTION99
2.9589-3.25640.22571450.17287021X-RAY DIFFRACTION99
3.2564-3.72690.17391440.15717046X-RAY DIFFRACTION99
3.7269-4.69290.15321360.14236787X-RAY DIFFRACTION96
4.6929-31.27210.16041410.14936873X-RAY DIFFRACTION96
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)
12.31053.4297-1.95426.3406-0.56078.6493-0.3234-0.3502-0.13740.03260.17320.4530.5148-0.00890.19770.169-0.0351-0.03940.1598-0.01320.2588-1.5987-7.412517.296
24.90.06561.63124.78422.33776.91030.02510.4432-0.5881-0.3113-0.1438-0.12490.73960.37470.10360.26810.0990.09020.2683-0.11510.307125.9335-8.20053.2616
31.5493-0.3979-0.27431.20840.09390.86270.00290.1685-0.182-0.1591-0.04150.16910.0923-0.13060.04190.1393-0.0121-0.00590.1433-0.02520.15182.83670.993510.3694
43.20482.8253-1.12977.2036-2.17123.1264-0.03830.0833-0.1053-0.0890.07240.05140.1196-0.0878-0.04740.1442-0.0241-0.00850.144-0.00870.12647.2099-28.193337.4267
51.02721.3063-1.50683.8918-3.11493.80490.0861-0.14750.02590.4235-0.1131-0.0371-0.09680.05840.06350.1883-0.0056-0.00710.1724-0.03760.114117.0683-11.276240.8304
65.06013.5812-0.42165.68480.4647.632-0.141-0.53440.24280.1726-0.0947-0.3725-0.50180.25560.1580.188-0.03270.06070.15050.05280.355528.585838.545815.1588
71.5046-0.55880.16331.1869-0.00321.02630.06150.20530.3071-0.2186-0.0673-0.1635-0.14330.06860.00830.16610.00020.03160.14780.0480.22621.263930.3378.2318
82.1633.30240.96296.25772.14151.12610.0375-0.02830.10.14510.07420.0116-0.05530.1035-0.11820.17190.008-0.00530.1636-0.0110.185515.368254.151335.5833
92.03792.28661.91374.98653.9524.9720.2224-0.347-0.04630.6686-0.1438-0.09770.157-0.0235-0.05590.276-0.0011-0.03750.1950.0390.196413.530944.491841.1255
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 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 418 )
5X-RAY DIFFRACTION5chain 'A' and (resid 419 through 501 )
6X-RAY DIFFRACTION6chain 'Z' and (resid 66 through 80 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 334 )
8X-RAY DIFFRACTION8chain 'B' and (resid 335 through 457 )
9X-RAY DIFFRACTION9chain 'B' and (resid 458 through 501 )

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