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- PDB-6ict: Structure of SETD3 bound to SAH and methylated actin -

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Basic information

Entry
Database: PDB / ID: 6ict
TitleStructure of SETD3 bound to SAH and methylated actin
Components
  • Actin, cytoplasmic 1
  • Histone-lysine N-methyltransferase setd3
KeywordsPROTEIN BINDING / histidine methylatransferase / Structural Genomics / Structural Genomics Consortium / SGC
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
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: 1.952 Å
AuthorsGuo, Q. / Liao, S. / Xu, C. / Structural Genomics Consortium (SGC)
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570737 China
National Natural Science Foundation of China31770806 China
CitationJournal: Elife / Year: 2019
Title: Structural insights into SETD3-mediated histidine methylation on beta-actin.
Authors: Guo, Q. / Liao, S. / Kwiatkowski, S. / Tomaka, W. / Yu, H. / Wu, G. / Tu, X. / Min, J. / Drozak, J. / Xu, C.
History
DepositionSep 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2019Group: Data collection / Database references / Polymer sequence
Category: citation / citation_author ...citation / citation_author / entity_poly / pdbx_database_related
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _entity_poly.pdbx_target_identifier
Revision 2.1Nov 22, 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
A: Histone-lysine N-methyltransferase setd3
B: Histone-lysine N-methyltransferase setd3
C: Histone-lysine N-methyltransferase setd3
D: Histone-lysine N-methyltransferase setd3
E: Actin, cytoplasmic 1
G: Actin, cytoplasmic 1
H: Actin, cytoplasmic 1
I: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,36212
Polymers242,8248
Non-polymers1,5384
Water20,0691114
1
A: Histone-lysine N-methyltransferase setd3
E: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0903
Polymers60,7062
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-17 kcal/mol
Surface area21870 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase setd3
G: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0903
Polymers60,7062
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-17 kcal/mol
Surface area21970 Å2
MethodPISA
3
C: Histone-lysine N-methyltransferase setd3
H: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0903
Polymers60,7062
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-18 kcal/mol
Surface area22060 Å2
MethodPISA
4
D: Histone-lysine N-methyltransferase setd3
I: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0903
Polymers60,7062
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-17 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.976, 176.693, 125.892
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Histone-lysine N-methyltransferase setd3 / SET domain-containing protein 3


Mass: 57824.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q86TU7, histone-lysine N-methyltransferase
#2: Protein/peptide
Actin, cytoplasmic 1 / Beta-actin


Mass: 2881.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P60709
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium acetate tetrahydrate 0.1M Sodium cacodylate trihydrate pH 6.5 20% Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→72.27 Å / Num. obs: 191350 / % possible obs: 99.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 8.1
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.868 / Num. unique obs: 27519

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMT

3smt


Resolution: 1.952→59.872 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 9084 4.85 %
Rwork0.1784 --
obs0.1801 187163 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→59.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15708 0 104 1114 16926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716232
X-RAY DIFFRACTIONf_angle_d0.87322049
X-RAY DIFFRACTIONf_dihedral_angle_d8.07213205
X-RAY DIFFRACTIONf_chiral_restr0.052454
X-RAY DIFFRACTIONf_plane_restr0.0062807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9517-1.97390.28432790.2545992X-RAY DIFFRACTION100
1.9739-1.99710.28193160.23716026X-RAY DIFFRACTION100
1.9971-2.02150.24843130.22265834X-RAY DIFFRACTION100
2.0215-2.0470.25363240.20275991X-RAY DIFFRACTION100
2.047-2.0740.2513410.19735909X-RAY DIFFRACTION99
2.074-2.10240.22542790.195893X-RAY DIFFRACTION98
2.1024-2.13240.24192840.19065724X-RAY DIFFRACTION95
2.1324-2.16430.26092840.195746X-RAY DIFFRACTION96
2.1643-2.19810.24742850.18945932X-RAY DIFFRACTION100
2.1981-2.23410.23773610.18765953X-RAY DIFFRACTION100
2.2341-2.27260.23563100.18585938X-RAY DIFFRACTION100
2.2726-2.3140.23173190.18155964X-RAY DIFFRACTION100
2.314-2.35850.22552980.17755956X-RAY DIFFRACTION100
2.3585-2.40660.23383070.18116035X-RAY DIFFRACTION100
2.4066-2.4590.2272900.17935953X-RAY DIFFRACTION100
2.459-2.51620.22452850.17536032X-RAY DIFFRACTION100
2.5162-2.57910.2072900.1765930X-RAY DIFFRACTION100
2.5791-2.64880.21843150.17585962X-RAY DIFFRACTION100
2.6488-2.72680.23143030.18215992X-RAY DIFFRACTION99
2.7268-2.81480.22312980.18185920X-RAY DIFFRACTION99
2.8148-2.91540.22763070.19055935X-RAY DIFFRACTION99
2.9154-3.03210.24993100.19475829X-RAY DIFFRACTION97
3.0321-3.17010.23242960.18445784X-RAY DIFFRACTION96
3.1701-3.33720.22262890.18546025X-RAY DIFFRACTION100
3.3372-3.54630.19992940.17115982X-RAY DIFFRACTION100
3.5463-3.820.18272930.1546009X-RAY DIFFRACTION100
3.82-4.20440.17692950.15536012X-RAY DIFFRACTION100
4.2044-4.81250.17492960.15075943X-RAY DIFFRACTION99
4.8125-6.06240.18363170.17885883X-RAY DIFFRACTION97
6.0624-59.90030.20433060.18645995X-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)
10.62580.1789-0.20840.7143-0.22440.60230.117-0.17130.15530.1672-0.0776-0.0074-0.12330.08580.02540.1948-0.04830.00420.1803-0.04290.16257.264214.113723.2428
20.9191-0.37840.0211.5243-0.30150.44010.09470.15170.1573-0.1979-0.1226-0.0417-0.0571-0.07610.02430.220.0355-0.01320.1983-0.03030.207214.507336.353-3.4414
30.69390.0430.06760.76070.06890.67880.0297-0.10390.1720.1302-0.023-0.006-0.06880.0325-0.0060.1326-0.01420.00760.1401-0.0190.16110.73914.8375-38.6532
40.5616-0.6980.13421.6141-0.35380.19940.12680.11090.0268-0.3474-0.1440.0724-0.0086-0.04740.02150.30750.0413-0.03620.2144-0.00080.255517.673935.8734-66.8282
50.76340.07360.10260.65050.00980.65960.0594-0.1391-0.17780.0932-0.0386-0.03230.0818-0.05310.00540.1109-0.0213-0.01030.11440.04330.104326.4295-15.3444-38.8952
60.6424-0.4986-0.25861.29740.52180.51520.07520.1237-0.0863-0.2909-0.050.01410.01350.0163-0.0250.2950.02430.00280.2341-0.01020.206919.8655-35.3563-67.5367
70.75530.0280.02710.6830.06130.51150.0254-0.1861-0.18960.0931-0.0407-0.02870.0966-0.0061-0.09880.1546-0.0219-0.00790.16610.07030.159723.266-15.982621.3582
80.8253-0.3938-0.09161.52870.52430.63340.03040.1217-0.1415-0.1529-0.0310.11310.04260.0726-0.00240.21780.0044-0.00470.1740.020.141815.6422-35.5053-6.1747
90.3695-0.4101-0.63942.01250.30691.2269-0.02410.12860.0257-0.03-0.03340.4049-0.144-0.31510.21770.207-0.05340.0287-0.0755-0.07270.30124.201125.2919.7738
100.593-0.6101-0.66721.8496-0.20111.42640.07870.1090.0023-0.0122-0.02470.3828-0.1268-0.23990.11130.15620.02160.00870.08390.0030.29947.22125.4229-43.1991
110.4194-0.34030.69171.44090.18771.639-0.05750.0359-0.09760.13280.0625-0.25670.26180.27450.17720.21780.02880.01450.11620.03660.210229.7156-26.5556-43.286
120.414-0.55720.53112.05610.04551.14110.07510.0369-0.11480.0030.0013-0.29510.21120.25160.22870.190.0207-0.05720.03570.1230.343225.185-26.607316.8932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 335 )
2X-RAY DIFFRACTION2chain 'A' and (resid 336 through 501 )
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 335 )
4X-RAY DIFFRACTION4chain 'B' and (resid 336 through 501 )
5X-RAY DIFFRACTION5chain 'C' and (resid 20 through 335 )
6X-RAY DIFFRACTION6chain 'C' and (resid 336 through 500 )
7X-RAY DIFFRACTION7chain 'D' and (resid 20 through 335 )
8X-RAY DIFFRACTION8chain 'D' and (resid 336 through 500 )
9X-RAY DIFFRACTION9chain 'E' and (resid 67 through 85 )
10X-RAY DIFFRACTION10chain 'G' and (resid 67 through 84 )
11X-RAY DIFFRACTION11chain 'H' and (resid 67 through 85 )
12X-RAY DIFFRACTION12chain 'I' and (resid 69 through 84 )

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