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- PDB-7w29: Crystal Structure of SETD3-SAH in complex with betaA-Orn73 peptide -

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Basic information

Entry
Database: PDB / ID: 7w29
TitleCrystal Structure of SETD3-SAH in complex with betaA-Orn73 peptide
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Histone-lysine N-methyltransferase setd3
KeywordsSTRUCTURAL PROTEIN / SET domain
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 / bBAF complex / cellular response to cytochalasin B / 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 / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / histone H3K36 methyltransferase activity / regulation of transepithelial transport / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBAF complex / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / 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 / 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 / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / 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 / B-WICH complex positively regulates rRNA expression / kinetochore / 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
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 ...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
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: 2.9 Å
AuthorsLi, H. / Ma, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Sci. / Year: 2022
Title: Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin.
Authors: Hintzen, J.C.J. / Ma, H. / Deng, H. / Witecka, A. / Andersen, S.B. / Drozak, J. / Guo, H. / Qian, P. / Li, H. / Mecinovic, J.
History
DepositionNov 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Actin, cytoplasmic 1, N-terminally processed
A: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4873
Polymers59,1022
Non-polymers3841
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-11 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.467, 77.668, 112.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Actin, cytoplasmic 1, N-terminally processed


Mass: 1879.095 Da / Num. of mol.: 1 / 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: 57223.000 Da / Num. of mol.: 1 / Fragment: SETD3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3 / Plasmid: pSUMOH10 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20%(w/v) PEG6000, 0.1M Bicine/Sodium hydroxide 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 11695 / % possible obs: 95.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.12 / Rrim(I) all: 0.269 / Χ2: 0.95 / Net I/σ(I): 2.9 / Num. measured all: 59662
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.954.90.5525920.7720.2720.6170.626100
2.95-350.4935870.820.240.550.68899.3
3-3.065.10.4855950.8390.2350.5410.61299.8
3.06-3.125.80.4655960.8480.2130.5120.64100
3.12-3.195.90.4456150.860.2010.4890.65799.7
3.19-3.2760.4055850.8860.1840.4460.705100
3.27-3.355.90.3576110.9040.1630.3940.73799.8
3.35-3.445.70.3325930.8790.1560.3680.80298.8
3.44-3.545.30.3016070.9110.1450.3360.8699
3.54-3.655.50.2895890.8870.1390.3220.95797.5
3.65-3.785.50.2685800.9060.1280.2990.89695.6
3.78-3.945.30.265550.9250.1280.2920.94793.1
3.94-4.114.90.2525700.9080.1290.2851.0691.9
4.11-4.334.40.2165440.9250.1180.2481.16289.5
4.33-4.64.80.2155320.9260.1160.2461.14187.8
4.6-4.964.60.1955490.9240.1070.2241.22888
4.96-5.464.60.1895700.9460.1030.2171.14890.8
5.46-6.244.90.1835910.9540.0940.2071.2195
6.24-7.864.30.1426110.9690.0780.1631.57194.1
7.86-503.50.086230.9890.0510.0962.37389.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MBJ

6mbj


Resolution: 2.9→47.71 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 1153 9.91 %
Rwork0.237 10483 -
obs0.2412 11636 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 39.7263 Å2 / Biso min: 24.82 Å2
Refinement stepCycle: final / Resolution: 2.9→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 26 38 4057
Biso mean--41.67 35.12 -
Num. residues----491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.030.34031390.27061318145797
3.03-3.190.27381340.266213631497100
3.19-3.390.30991490.25313531502100
3.39-3.650.30131390.23271347148698
3.65-4.010.27971460.23251279142594
4.01-4.590.25691360.22181225136189
4.59-5.790.27541590.23341250140990
5.79-47.710.25561510.22671348149991

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