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- PDB-6icv: Structure of SETD3 bound to SAH and unmodified actin -

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Basic information

Entry
Database: PDB / ID: 6icv
TitleStructure of SETD3 bound to SAH and unmodified 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 / regulation of transepithelial transport ...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 / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / histone H3K36 methyltransferase activity / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / regulation of double-strand break repair / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / histone H3K4 methyltransferase activity / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / 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 / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of muscle cell differentiation / positive regulation of double-strand break repair / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / brush border / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / actin filament / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / PKMTs methylate histone lysines / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / tau protein binding / VEGFA-VEGFR2 Pathway / platelet aggregation / cytoplasmic ribonucleoprotein granule / nuclear matrix / 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 / Signaling by BRAF and RAF1 fusions
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: 2.15 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 ...Data collection / Database references / Other / Polymer sequence / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_poly / pdbx_SG_project / pdbx_database_related / pdbx_database_status / struct_keywords
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 / _pdbx_database_status.SG_entry / _struct_keywords.text
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

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase setd3
C: Actin, cytoplasmic 1
B: Histone-lysine N-methyltransferase setd3
D: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1556
Polymers121,3864
Non-polymers7692
Water10,647591
1
A: Histone-lysine N-methyltransferase setd3
C: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0773
Polymers60,6932
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-14 kcal/mol
Surface area21900 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase setd3
D: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0773
Polymers60,6932
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-14 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.186, 175.170, 66.499
Angle α, β, γ (deg.)90.00, 92.57, 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.: 2
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: 2868.247 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES sodium pH 7.5 2% Polyethylene glycol 400 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. obs: 74952 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 14
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.609 / Num. unique obs: 5708

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMT

3smt


Resolution: 2.15→32.634 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.205 3629 5.04 %
Rwork0.1675 --
obs0.1695 71998 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→32.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 52 591 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078097
X-RAY DIFFRACTIONf_angle_d0.83611008
X-RAY DIFFRACTIONf_dihedral_angle_d7.7856567
X-RAY DIFFRACTIONf_chiral_restr0.0481226
X-RAY DIFFRACTIONf_plane_restr0.0061405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1429-2.1710.26771080.19642028X-RAY DIFFRACTION75
2.171-2.20080.2321970.18092288X-RAY DIFFRACTION82
2.2008-2.23220.31091190.19012336X-RAY DIFFRACTION85
2.2322-2.26550.22031110.19082343X-RAY DIFFRACTION86
2.2655-2.30090.2431260.17732434X-RAY DIFFRACTION89
2.3009-2.33860.26291460.18492485X-RAY DIFFRACTION91
2.3386-2.37890.24511050.1892612X-RAY DIFFRACTION93
2.3789-2.42220.25821330.18452611X-RAY DIFFRACTION96
2.4222-2.46880.24881430.18142632X-RAY DIFFRACTION96
2.4688-2.51910.21931340.17992693X-RAY DIFFRACTION99
2.5191-2.57390.21621590.18262720X-RAY DIFFRACTION99
2.5739-2.63370.23431610.18422723X-RAY DIFFRACTION100
2.6337-2.69960.22651480.18932748X-RAY DIFFRACTION100
2.6996-2.77250.2281400.18522741X-RAY DIFFRACTION100
2.7725-2.85410.23891310.18362757X-RAY DIFFRACTION100
2.8541-2.94610.22491510.17922731X-RAY DIFFRACTION100
2.9461-3.05130.20061380.18342760X-RAY DIFFRACTION100
3.0513-3.17340.22521520.18152755X-RAY DIFFRACTION100
3.1734-3.31770.22511460.17882738X-RAY DIFFRACTION100
3.3177-3.49240.20991630.16032733X-RAY DIFFRACTION100
3.4924-3.7110.18171410.15492736X-RAY DIFFRACTION100
3.711-3.9970.16581710.1372746X-RAY DIFFRACTION100
3.997-4.39840.1661550.13052730X-RAY DIFFRACTION100
4.3984-5.03290.1541580.14062745X-RAY DIFFRACTION100
5.0329-6.33330.20151300.17082764X-RAY DIFFRACTION100
6.3333-32.63820.18791630.16972780X-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)
12.2160.14340.72822.32860.2993.75190.04860.4026-0.3562-0.37030.0228-0.3550.65220.4152-0.08070.28690.07390.06120.292-0.08610.280725.6036-7.29913.156
21.3648-0.3618-0.31061.18780.18530.66670.04350.1434-0.1418-0.1491-0.04790.11670.0705-0.09710.01110.1533-0.0054-0.02270.1629-0.02550.1412.52451.684610.7556
32.07070.8745-0.10574.0917-0.86421.8992-0.06880.1152-0.1707-0.19190.08350.0660.1128-0.0432-0.0220.2408-0.02330.00280.2207-0.01670.16766.9461-27.505337.346
40.58980.4719-0.54282.3754-1.71642.48450.0369-0.1473-0.02820.4102-0.0428-0.0898-0.0825-0.02870.0150.2159-0.0009-0.02730.188-0.02390.120316.8271-10.568740.4986
54.4773-1.5078-2.28282.96051.05015.3524-0.241-0.0191-0.40890.08380.10510.23530.4645-0.08610.13790.231-0.0431-0.01330.15090.0050.22611.6579-9.191215.2385
61.3229-0.48820.16541.1518-0.03260.89610.11010.18620.302-0.2434-0.0645-0.1217-0.1060.0325-0.03640.19130.00410.03440.17370.04830.245821.39730.65518.3481
72.5041.62470.37213.51390.66951.73530.00390.0920.08320.00750.02530.0765-0.02750.0515-0.0290.2554-0.02970.0120.2317-0.03460.244220.090360.648634.6472
81.28021.00610.15982.87650.88121.47720.194-0.28950.08790.4669-0.20120.1172-0.00690.00130.00870.2396-0.01080.02540.21140.00490.1929.344743.530137.8539
95.14510.90071.96240.25820.55313.4071-0.2513-0.06170.7045-0.0379-0.0299-0.4736-0.52320.10630.28870.2603-0.02730.06380.12540.02080.410225.273740.857812.8322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 335 )
3X-RAY DIFFRACTION3chain 'A' and (resid 336 through 419 )
4X-RAY DIFFRACTION4chain 'A' and (resid 420 through 502 )
5X-RAY DIFFRACTION5chain 'C' and (resid 67 through 83 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 335 )
7X-RAY DIFFRACTION7chain 'B' and (resid 336 through 419 )
8X-RAY DIFFRACTION8chain 'B' and (resid 420 through 501 )
9X-RAY DIFFRACTION9chain 'D' and (resid 67 through 83 )

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