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- PDB-3s7j: Structural Basis of Substrate Methylation and Inhibition of SMYD2 -

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Basic information

Entry
Database: PDB / ID: 3s7j
TitleStructural Basis of Substrate Methylation and Inhibition of SMYD2
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE / Methyltransferase / p53
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / : / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...SMYD2, SET domain / : / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.04 Å
AuthorsFerguson, A.D.
CitationJournal: Structure / Year: 2011
Title: Structural Basis of Substrate Methylation and Inhibition of SMYD2.
Authors: Ferguson, A.D. / Larsen, N.A. / Howard, T. / Pollard, H. / Green, I. / Grande, C. / Cheung, T. / Garcia-Arenas, R. / Cowen, S. / Wu, J. / Godin, R. / Chen, H. / Keen, N.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4275
Polymers49,8321
Non-polymers5954
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.565, 154.565, 53.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein N-lysine methyltransferase SMYD2 / HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain- ...HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain-containing protein 2


Mass: 49832.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.2805 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2805 Å / Relative weight: 1
ReflectionResolution: 3.04→109.39 Å / Num. obs: 12111 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.5 % / Biso Wilson estimate: 90.38 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 25.1
Reflection shellResolution: 3.04→3.34 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.04→48.88 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.9148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 584 4.82 %RANDOM
Rwork0.1937 ---
all0.1944 ---
obs0.1944 10997 98.15 %-
Displacement parametersBiso mean: 82.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.7337 Å20 Å20 Å2
2---2.7337 Å20 Å2
3---5.4673 Å2
Refine analyzeLuzzati coordinate error obs: 0.636 Å
Refinement stepCycle: LAST / Resolution: 3.04→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 30 0 3479
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013557HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.254798HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d01277SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes097HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0506HARMONIC5
X-RAY DIFFRACTIONt_it03557HARMONIC20
X-RAY DIFFRACTIONt_nbd00SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion21.97
X-RAY DIFFRACTIONt_chiral_improper_torsion0446SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact03896SEMIHARMONIC4
LS refinement shellResolution: 3.04→3.33 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2553 132 4.92 %
Rwork0.2329 2551 -
all0.234 2683 -
obs--98.15 %
Refinement TLS params.Method: refined / Origin x: 50.6261 Å / Origin y: 20.5606 Å / Origin z: 54.1704 Å
111213212223313233
T-0.1747 Å20.2101 Å20.035 Å2--0.0184 Å20.112 Å2---0.312 Å2
L1.5641 °2-0.2207 °2-0.2967 °2-3.3413 °2-0.6199 °2--3.5957 °2
S0.059 Å °-0.1316 Å °-0.0285 Å °0.1548 Å °-0.1499 Å °-0.2708 Å °-0.6924 Å °-0.4066 Å °0.0909 Å °

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