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- PDB-5ex3: Crystal structure of human SMYD3 in complex with a VEGFR1 peptide -

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Basic information

Entry
Database: PDB / ID: 5ex3
TitleCrystal structure of human SMYD3 in complex with a VEGFR1 peptide
Components
  • Histone-lysine N-methyltransferase SMYD3
  • VEGFR1 peptide
KeywordsTRANSFERASE / SET domain / methylation / chromatin / cancer
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / histone H3K36 dimethyltransferase activity / hyaloid vascular plexus regression / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / histone H3K36 dimethyltransferase activity / hyaloid vascular plexus regression / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / histone H3K4 trimethyltransferase activity / embryonic morphogenesis / sprouting angiogenesis / blood vessel morphogenesis / negative regulation of vascular endothelial cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / growth factor binding / positive regulation of MAP kinase activity / monocyte chemotaxis / RNA polymerase II complex binding / cellular response to vascular endothelial growth factor stimulus / cellular response to dexamethasone stimulus / vascular endothelial growth factor receptor signaling pathway / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation / establishment of protein localization / receptor protein-tyrosine kinase / PKMTs methylate histone lysines / positive regulation of angiogenesis / cell migration / nucleosome assembly / actin cytoskeleton / protein autophosphorylation / methylation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / endosome / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / focal adhesion / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Vascular endothelial growth factor receptor 1 (VEGFR1) / 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. / : / VEGFR-2, transmembrane domain / : ...Vascular endothelial growth factor receptor 1 (VEGFR1) / 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. / : / VEGFR-2, transmembrane domain / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Beta-clip-like / SET domain / Annexin V; domain 1 / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Immunoglobulin / Immunoglobulin domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Helix non-globular / Beta Complex / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Special / Immunoglobulin V-set domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tetratricopeptide-like helical domain superfamily / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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 / Vascular endothelial growth factor receptor 1 / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.408 Å
AuthorsQiao, Q. / Fu, W. / Liu, N. / 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 program of CASXDB08010100 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 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SMYD3
D: VEGFR1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78510
Polymers50,9642
Non-polymers8218
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.378, 104.659, 117.599
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: 49962.980 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: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIPL
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase
#2: Protein/peptide VEGFR1 peptide


Mass: 1001.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P17948*PLUS

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Non-polymers , 4 types, 104 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


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.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.8M NaAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 26005 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 53.17 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.07 / Net I/av σ(I): 13.014 / Net I/σ(I): 13.3 / Num. measured all: 179578
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.497.10.52925391.147100
2.49-2.5970.38925511.131100
2.59-2.770.31225551.176100
2.7-2.8570.22925731.113100
2.85-3.0270.17525631.094100
3.02-3.2670.13825941.019100
3.26-3.5870.11625970.994100
3.58-4.16.90.10926040.975100
4.1-5.166.80.12226461.034100
5.16-306.30.09427831.01299.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.6_289)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.408→30 Å / FOM work R set: 0.8156 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1922 7.71 %Random selection
Rwork0.1843 23003 --
obs0.1874 24925 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.744 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 152.26 Å2 / Biso mean: 65.21 Å2 / Biso min: 38.81 Å2
Baniso -1Baniso -2Baniso -3
1-6.1519 Å20 Å2-0 Å2
2--9.6147 Å20 Å2
3----15.7666 Å2
Refinement stepCycle: final / Resolution: 2.408→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 45 96 3617
Biso mean--75.58 65.41 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083596
X-RAY DIFFRACTIONf_angle_d1.1534838
X-RAY DIFFRACTIONf_chiral_restr0.075528
X-RAY DIFFRACTIONf_plane_restr0.004628
X-RAY DIFFRACTIONf_dihedral_angle_d19.4681384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4081-2.49410.29521560.23951875203180
2.4941-2.5940.31181790.23472147232691
2.594-2.71190.30181890.22762220240993
2.7119-2.85480.2931860.22992265245195
2.8548-3.03350.30561920.22342317250997
3.0335-3.26750.25341990.20922359255898
3.2675-3.59580.24112020.18052389259199
3.5958-4.1150.19732000.1522411261199
4.115-5.18010.16262040.139524552659100
5.1801-30.00530.20732150.19242565278099

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