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- PDB-6jat: Crystal structure of SETD3 bound to Actin peptide and SFG -

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Basic information

Entry
Database: PDB / ID: 6jat
TitleCrystal structure of SETD3 bound to Actin peptide and SFG
Components
  • Actin, gamma-enteric smooth muscle
  • Histone-lysine N-methyltransferase setd3
KeywordsTRANSFERASE / SET domain
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 / dynactin complex / histone H3K36 methyltransferase activity / myosin filament / histone H3K4 methyltransferase activity / mesenchyme migration ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / dynactin complex / histone H3K36 methyltransferase activity / myosin filament / histone H3K4 methyltransferase activity / mesenchyme migration / positive regulation of muscle cell differentiation / Smooth Muscle Contraction / filopodium / muscle contraction / cell periphery / PKMTs methylate histone lysines / lamellipodium / actin binding / cell body / blood microparticle / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromatin / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / cytosol / cytoplasm
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
SINEFUNGIN / Actin, gamma-enteric smooth muscle / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.713 Å
AuthorsLi, H. / Zheng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)91753203 China
CitationJournal: to be published
Title: Crystal structure of SETD3 bound to Actin peptide and SFG
Authors: Li, H. / Zheng, Y.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: Actin, gamma-enteric smooth muscle
C: Histone-lysine N-methyltransferase setd3
D: Actin, gamma-enteric smooth muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,07512
Polymers119,5944
Non-polymers1,4818
Water1,51384
1
A: Histone-lysine N-methyltransferase setd3
B: Actin, gamma-enteric smooth muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4676
Polymers59,7972
Non-polymers6704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-57 kcal/mol
Surface area22880 Å2
MethodPISA
2
C: Histone-lysine N-methyltransferase setd3
D: Actin, gamma-enteric smooth muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6096
Polymers59,7972
Non-polymers8124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-42 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.434, 131.282, 175.153
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

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


Mass: 57223.000 Da / Num. of mol.: 2 / Fragment: SETD3 protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Plasmid: pSUMOH10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q86TU7, histone-lysine N-methyltransferase
#2: Protein/peptide Actin, gamma-enteric smooth muscle / / Alpha-actin-3 / Gamma-2-actin / Smooth muscle gamma-actin


Mass: 2573.942 Da / Num. of mol.: 2 / Fragment: Actin peptide / Source method: obtained synthetically / Details: chemical synthesized peptide 60-81 / Source: (synth.) Homo sapiens (human) / References: UniProt: P63267

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Non-polymers , 4 types, 92 molecules

#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.9 Å3/Da / Density % sol: 57.66 % / Mosaicity: 0.778 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M HEPES/Sodium hydroxide, 0.2 M Ammonium sulfate, 20% PEG 8000, 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 29, 2018 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 38336 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.055 / Rrim(I) all: 0.172 / Χ2: 0.862 / Net I/σ(I): 4.4 / Num. measured all: 370511
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.769.20.85524990.8280.2970.9070.47899.8
2.76-2.838.80.66325130.8720.2370.7060.52799.8
2.83-2.918.60.62225060.8890.2250.6640.51199.8
2.91-2.9910.20.53825320.9340.1780.5670.54499.9
2.99-3.0910.10.45825080.9410.1530.4830.555100
3.09-3.210.30.35725240.9670.1170.3770.626100
3.2-3.3310.20.28725590.980.0940.3020.701100
3.33-3.4810.20.23325230.9850.0770.2460.836100
3.48-3.6610.10.18725280.9880.0620.1970.971100
3.66-3.899.80.15625470.990.0520.1651.08299.7
3.89-4.198.70.1325490.9920.0460.1381.16199.2
4.19-4.629.80.11225830.9940.0380.1181.2499.8
4.62-5.2810.30.10225700.9960.0330.1071.07599.9
5.28-6.65100.09326340.9960.0310.0980.91299.9
6.65-508.70.06627610.9970.0240.0711.67699.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.545
Highest resolutionLowest resolution
Rotation46.15 Å2.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMT
Resolution: 2.713→49.74 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2429 1944 5.08 %
Rwork0.1995 --
obs0.2018 38266 99.04 %
Displacement parametersBiso max: 93.45 Å2 / Biso mean: 46.2428 Å2 / Biso min: 24.52 Å2
Refinement stepCycle: LAST / Resolution: 2.713→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7957 0 94 84 8135

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