- PDB-3tg5: Structure of SMYD2 in complex with p53 and SAH -
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Basic information
Entry
Database: PDB / ID: 3tg5
Title
Structure of SMYD2 in complex with p53 and SAH
Components
Cellular tumor antigen p53
N-lysine methyltransferase SMYD2
Keywords
TRANSFERASE / SET domain / methyltransferase / co factor binding
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 / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator ...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 / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / histone H3 methyltransferase activity / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / ER overload response / negative regulation of DNA replication / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / RNA polymerase II complex binding / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / mitophagy / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / neuroblast proliferation / : / negative regulation of reactive oxygen species metabolic process / hematopoietic stem cell differentiation / chromosome organization / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / embryonic organ development / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / cellular response to glucose starvation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / negative regulation of fibroblast proliferation Similarity search - Function
Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein
N-lysinemethyltransferaseSMYD2 / 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: 49760.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pFastbac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
Resolution: 2.3→29.75 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.864 / SU B: 7.732 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26317
1042
5.1 %
RANDOM
Rwork
0.24101
-
-
-
all
0.24215
20353
-
-
obs
0.24215
19311
100 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 37.321 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.29 Å2
0 Å2
0 Å2
2-
-
-0.28 Å2
0 Å2
3-
-
-
1.57 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→29.75 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3472
0
35
209
3716
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.022
3581
X-RAY DIFFRACTION
r_angle_refined_deg
0.988
1.977
4823
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.799
5
431
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.24
24.277
166
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.752
15
658
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.692
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.071
0.2
515
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
2681
LS refinement shell
Resolution: 2.3→2.359 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.314
72
-
Rwork
0.267
1322
-
obs
-
-
100 %
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