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- PDB-5ex0: Crystal structure of human SMYD3 in complex with a MAP3K2 peptide -

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Basic information

Entry
Database: PDB / ID: 5ex0
TitleCrystal structure of human SMYD3 in complex with a MAP3K2 peptide
Components
  • Histone-lysine N-methyltransferase SMYD3
  • MAP3K2 peptide
KeywordsTRANSFERASE / SET domain / methylation / chromatin / cancer
Function / homology
Function and homology information


histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / mitogen-activated protein kinase kinase kinase / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / MAP kinase kinase kinase activity / cellular response to dexamethasone stimulus ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / mitogen-activated protein kinase kinase kinase / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / MAP kinase kinase kinase activity / cellular response to dexamethasone stimulus / establishment of protein localization / cellular response to mechanical stimulus / PKMTs methylate histone lysines / nucleosome assembly / methylation / protein kinase activity / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / PB1 domain / PB1 domain ...Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Annexin V; domain 1 / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Helix non-globular / Beta Complex / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase SMYD3 / Mitogen-activated protein kinase kinase kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFu, W. / Liu, N. / Qiao, Q. / Wang, M. / Min, J. / Zhu, B. / Xu, R.M. / Yang, N.
Funding support China, 6items
OrganizationGrant numberCountry
MOST2015CB856200 China
National Natural Science Foundation of China31521002 China
National Natural Science Foundation of China31430018 China
National Natural Science Foundation of China31210103914 China
Strategic priority Research ProgramXDB08010100 China
National Key New Drug Creation and Manufacturing Program of China2014ZX09507002 China
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase
Authors: Fu, W. / Liu, N. / Qiao, Q. / Wang, M. / Min, J. / Zhu, B. / Xu, R.M. / Yang, N.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 SMYD3
D: MAP3K2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3278
Polymers50,6272
Non-polymers7016
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-7 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.598, 104.181, 117.215
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, 2 molecules AD

#1: Protein Histone-lysine N-methyltransferase SMYD3 / SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 49541.492 Da / Num. of mol.: 1 / Mutation: K13N, K140R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Plasmid: pET28a-smt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase
#2: Protein/peptide MAP3K2 peptide


Mass: 1085.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2U5*PLUS

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Non-polymers , 4 types, 123 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.4M NaAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18908 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 40.89 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.049 / Rrim(I) all: 0.121 / Χ2: 0.928 / Net I/av σ(I): 15.755 / Net I/σ(I): 7.4 / Num. measured all: 113209
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.86.20.73218400.8030.320.80.985100
2.8-2.916.10.53718360.870.2360.5880.95699.9
2.91-3.046.10.38718670.9310.170.4230.928100
3.04-3.26.10.27418630.9620.120.30.906100
3.2-3.46.10.17118820.9840.0750.1870.868100
3.4-3.666.10.12218730.9910.0540.1340.881100
3.66-4.0360.08918830.9930.040.0970.886100
4.03-4.625.90.0819000.9950.0360.0881.17399.9
4.62-5.815.70.07519280.9940.0340.0821.10399.9
5.81-505.50.04120360.9970.0190.0450.59599.5

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MEK

3mek


Resolution: 2.7→47.66 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.55 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 938 5.14 %Random selection
Rwork0.1779 17323 --
obs0.1803 18261 96.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.53 Å2 / Biso mean: 36.4011 Å2 / Biso min: 17.9 Å2
Refinement stepCycle: final / Resolution: 2.7→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 37 117 3658
Biso mean--33.9 36.21 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043627
X-RAY DIFFRACTIONf_angle_d0.7984886
X-RAY DIFFRACTIONf_chiral_restr0.032532
X-RAY DIFFRACTIONf_plane_restr0.003633
X-RAY DIFFRACTIONf_dihedral_angle_d13.4381410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.82920.34331120.25821924203677
2.8292-3.00640.29241250.22472506263199
3.0064-3.23850.26951530.208524962649100
3.2385-3.56430.23351430.17925542697100
3.5643-4.07980.20511350.15925522687100
4.0798-5.13920.18161410.143325822723100
5.1392-47.66790.20381290.17672709283899

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