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- PDB-7w28: Crystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide -

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Basic information

Entry
Database: PDB / ID: 7w28
TitleCrystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide
Components
  • Actin, cytoplasmic 1
  • 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 / 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 / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / histone H3K36 methyltransferase activity / Formation of annular gap junctions / Gap junction degradation / regulation of G0 to G1 transition / Tat protein binding / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / apical protein localization / RSC-type complex / adherens junction assembly / Adherens junctions interactions / RHOF GTPase cycle / histone H3K4 methyltransferase activity / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of double-strand break repair / positive regulation of T cell differentiation / regulation of norepinephrine uptake / apical junction complex / nitric-oxide synthase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of muscle cell differentiation / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / kinesin binding / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / substantia nigra development / calyx of Held / EPHB-mediated forward signaling / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / cell motility / regulation of transmembrane transporter activity / Signaling by high-kinase activity BRAF mutants / DNA Damage Recognition in GG-NER / MAP2K and MAPK activation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / tau protein binding / B-WICH complex positively regulates rRNA expression / kinetochore / structural constituent of cytoskeleton / PKMTs methylate histone lysines / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / cytoplasmic ribonucleoprotein granule / VEGFA-VEGFR2 Pathway / 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 / actin cytoskeleton
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 superfamily / SET domain profile. ...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
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: 1.79 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 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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
P: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7135
Polymers59,1362
Non-polymers5773
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-35 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.527, 43.413, 96.048
Angle α, β, γ (deg.)90.000, 101.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: 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
#2: Protein/peptide Actin, cytoplasmic 1 / Beta-actin


Mass: 1913.111 Da / Num. of mol.: 1 / Fragment: SAH / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30%(w/v) PEG4000, 0.1 M Tris base/Hydrochloric acid 8.5, 0.2M Lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 22, 2020 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 49400 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.062 / Rrim(I) all: 0.138 / Χ2: 1.805 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.10.56624370.8230.2740.6310.52398.5
1.83-1.864.90.49424550.8310.2460.5530.53998.6
1.86-1.94.70.41224330.8720.2090.4630.57898
1.9-1.945.20.38424190.90.1840.4270.64399.1
1.94-1.985.40.32124870.9270.150.3550.71699.2
1.98-2.035.40.28124290.9460.1320.3110.79498.8
2.03-2.085.40.24724520.9480.1160.2740.91198.8
2.08-2.135.30.22324210.9580.1050.2471.09399.1
2.13-2.25.30.19624790.9660.0940.2181.25399.2
2.2-2.275.20.18524510.9670.0890.2061.3799.4
2.27-2.3550.17224750.9670.0850.1931.60999.2
2.35-2.444.70.15924670.9690.0820.181.85799.4
2.44-2.555.40.15624910.970.0750.1732.04199.7
2.55-2.695.40.14624560.9770.070.1632.24799.5
2.69-2.865.30.13724900.9790.0660.1522.65699.5
2.86-3.085.20.12724890.9810.0620.1422.8999.6
3.08-3.394.70.11524820.9780.0610.1313.37699.4
3.39-3.884.70.10125070.9830.0530.1143.70698.9
3.88-4.884.90.09725180.9860.050.113.96999.1
4.88-504.60.09825620.9880.0510.1113.898.1

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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: 1.79→38.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 2406 4.87 %
Rwork0.1743 46984 -
obs0.1762 49390 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.04 Å2 / Biso mean: 36.7786 Å2 / Biso min: 14.09 Å2
Refinement stepCycle: final / Resolution: 1.79→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 36 514 4567
Biso mean--36.95 40.67 -
Num. residues----494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.830.28061280.23422434256288
1.83-1.870.25941330.22432754288798
1.87-1.910.27461500.21392737288798
1.91-1.960.27111240.19492795291999
1.96-2.010.19981440.18912730287499
2.01-2.070.23481280.18452778290699
2.07-2.140.24981350.18872753288899
2.14-2.210.22261330.18492799293299
2.21-2.30.22651280.17892784291299
2.3-2.410.25741390.17982768290799
2.41-2.530.22551650.189827902955100
2.53-2.690.21231510.18822770292199
2.69-2.90.24221380.185828142952100
2.9-3.190.20931370.183528032940100
3.19-3.650.2121780.16762771294999
3.65-4.60.16991350.1412840297599
4.6-38.590.18421600.1622864302498
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)
10.90380.00550.72381.54760.91473.26490.0310.1754-0.0359-0.13440.2814-0.26230.25920.7084-0.1760.20280.0210.02030.3192-0.06390.2025-13.8871-8.509116.4462
21.00310.6429-0.33421.8474-0.52541.32410.0246-0.0231-0.02220.08460.00870.01950.0203-0.061-0.03480.13510.0063-0.01720.1377-0.01260.2028-29.5386-10.917747.8624
31.6159-1.9172-1.28534.159-0.3973.0523-0.2001-0.3457-0.07580.05840.22980.29680.8995-0.1348-0.05790.43690.0155-0.0280.18730.03870.1234-21.1761-17.543521.4969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 334 )A20 - 334
2X-RAY DIFFRACTION2chain 'A' and (resid 335 through 497 )A335 - 497
3X-RAY DIFFRACTION3chain 'P' and (resid 66 through 81 )P66 - 81

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