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- PDB-9ckc: Crystal structure of SMYD2 in complex with two PARP1 peptides -

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Basic information

Entry
Database: PDB / ID: 9ckc
TitleCrystal structure of SMYD2 in complex with two PARP1 peptides
Components
  • N-lysine methyltransferase SMYD2
  • Poly [ADP-ribose] polymerase 1, processed C-terminus
KeywordsTRANSFERASE / SMYD2 / PARP1 / Methyltransferase / SET and MYND-containing protein
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / peptidyl-lysine dimethylation / NAD+-protein-tyrosine ADP-ribosyltransferase activity ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / peptidyl-lysine dimethylation / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / histone H3K4 trimethyltransferase activity / mitochondrial DNA metabolic process / histone H3K36 methyltransferase activity / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / protein-lysine N-methyltransferase activity / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / signal transduction involved in regulation of gene expression / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / histone H3 methyltransferase activity / mitochondrial DNA repair / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / NAD+-protein-glutamate ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / cellular response to zinc ion / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear replication fork / decidualization / RNA polymerase II complex binding / protein autoprocessing / R-SMAD binding / site of DNA damage / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of transcription elongation by RNA polymerase II / POLB-Dependent Long Patch Base Excision Repair / positive regulation of SMAD protein signal transduction / NAD+ poly-ADP-ribosyltransferase activity / SUMOylation of DNA damage response and repair proteins / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / telomere maintenance / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / protein-DNA complex / cellular response to nerve growth factor stimulus / DNA Damage Recognition in GG-NER / Regulation of TP53 Activity through Methylation / protein modification process / Dual Incision in GG-NER / PKMTs methylate histone lysines / positive regulation of protein localization to nucleus / Formation of Incision Complex in GG-NER / histone deacetylase binding / cellular response to insulin stimulus / NAD binding / cellular response to amyloid-beta / cellular response to UV / p53 binding / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / heart development / cellular response to oxidative stress / transcription regulator complex / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II
Similarity search - Function
SMYD2, SET domain / : / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...SMYD2, SET domain / : / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / MYND finger / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Poly [ADP-ribose] polymerase 1 / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, Y. / Alshammari, E. / Spellmon, N. / Brunzelle, J. / Yang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Biorxiv / Year: 2024
Title: Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding.
Authors: Zhang, Y. / Alshammari, E. / Sobota, J. / Spellmon, N. / Perry, E. / Cao, T. / Mugunamalwaththa, T. / Smith, S. / Brunzelle, J. / Wu, G. / Stemmler, T. / Jin, J. / Li, C. / Yang, Z.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
B: N-lysine methyltransferase SMYD2
C: Poly [ADP-ribose] polymerase 1, processed C-terminus
D: Poly [ADP-ribose] polymerase 1, processed C-terminus
E: Poly [ADP-ribose] polymerase 1, processed C-terminus
F: Poly [ADP-ribose] polymerase 1, processed C-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,27614
Polymers105,1156
Non-polymers1,1618
Water7,566420
1
A: N-lysine methyltransferase SMYD2
C: Poly [ADP-ribose] polymerase 1, processed C-terminus
E: Poly [ADP-ribose] polymerase 1, processed C-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1387
Polymers52,5573
Non-polymers5814
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-7 kcal/mol
Surface area20610 Å2
MethodPISA
2
B: N-lysine methyltransferase SMYD2
D: Poly [ADP-ribose] polymerase 1, processed C-terminus
F: Poly [ADP-ribose] polymerase 1, processed C-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1387
Polymers52,5573
Non-polymers5814
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.792, 52.185, 144.916
Angle α, β, γ (deg.)90.000, 113.242, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHE(chain 'A' and (resid 5 through 34 or resid 36...AA5 - 345 - 34
12CYSCYSARGARG(chain 'A' and (resid 5 through 34 or resid 36...AA36 - 25036 - 250
13ASPASPARGARG(chain 'A' and (resid 5 through 34 or resid 36...AA252 - 306252 - 306
14ALAALALEULEU(chain 'A' and (resid 5 through 34 or resid 36...AA308 - 323308 - 323
15GLNGLNHISHIS(chain 'A' and (resid 5 through 34 or resid 36...AA325 - 433325 - 433
21GLYGLYPHEPHE(chain 'B' and (resid 5 through 34 or resid 36...BB5 - 345 - 34
22CYSCYSARGARG(chain 'B' and (resid 5 through 34 or resid 36...BB36 - 25036 - 250
23ASPASPARGARG(chain 'B' and (resid 5 through 34 or resid 36...BB252 - 306252 - 306
24ALAALALEULEU(chain 'B' and (resid 5 through 34 or resid 36...BB308 - 323308 - 323
25GLNGLNHISHIS(chain 'B' and (resid 5 through 34 or resid 36...BB325 - 433325 - 433

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pCDF-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide
Poly [ADP-ribose] polymerase 1, processed C-terminus / Poly [ADP-ribose] polymerase 1 / 89-kDa form


Mass: 1362.662 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P09874
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 100 mM Tris pH 7.5, 5% ethanol, 1 mM PARP1 peptide, 0.6 mM AdoHcy

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→133.16 Å / Num. obs: 57685 / % possible obs: 88.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.26 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.042 / Rrim(I) all: 0.114 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.137 Å / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 51097 / CC1/2: 0.772 / Rpim(I) all: 0.505 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→66.58 Å / SU ML: 0.2174 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.7534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2079 2578 5.05 %
Rwork0.1839 48501 -
obs0.1851 51079 88.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→66.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7067 0 58 420 7545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427303
X-RAY DIFFRACTIONf_angle_d0.7189842
X-RAY DIFFRACTIONf_chiral_restr0.04631052
X-RAY DIFFRACTIONf_plane_restr0.00451263
X-RAY DIFFRACTIONf_dihedral_angle_d14.14822794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.26961400.26492968X-RAY DIFFRACTION99.97
2.14-2.190.311610.2523041X-RAY DIFFRACTION99.81
2.19-2.230.2629790.25941642X-RAY DIFFRACTION91.98
2.28-2.340.28661400.23152719X-RAY DIFFRACTION92.82
2.34-2.410.23681760.21792987X-RAY DIFFRACTION99.97
2.41-2.480.22441550.21883047X-RAY DIFFRACTION100
2.48-2.560.2531790.2172992X-RAY DIFFRACTION99.97
2.56-2.650.25521640.21963039X-RAY DIFFRACTION100
2.65-2.750.24351020.22622120X-RAY DIFFRACTION69.76
2.75-2.880.24641620.21393046X-RAY DIFFRACTION100
2.88-3.030.26861710.21533030X-RAY DIFFRACTION99.84
3.03-3.220.21971550.21033034X-RAY DIFFRACTION99.97
3.22-3.470.21051410.18172693X-RAY DIFFRACTION87.82
3.47-3.820.17671490.15952863X-RAY DIFFRACTION94.3
3.82-4.370.1551590.14113025X-RAY DIFFRACTION98.18
4.37-5.510.16251750.13563083X-RAY DIFFRACTION99.94
5.51-66.580.17821700.16493172X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 4.65027952193 Å / Origin y: -11.6364638611 Å / Origin z: 31.917114236 Å
111213212223313233
T0.17311467657 Å2-0.0321676923398 Å2-0.0118999345867 Å2-0.164345520486 Å20.0133895276072 Å2--0.176799568313 Å2
L0.211141084172 °2-0.155274841532 °2-0.207836579634 °2-0.185131052415 °20.22474558159 °2--0.27322751455 °2
S-0.00886560022923 Å °0.0186360025156 Å °-0.0288223473517 Å °-0.00971421518219 Å °-0.017102871163 Å °0.0259958072511 Å °-0.00540884667804 Å °0.0226124797701 Å °-2.26395582269E-5 Å °
Refinement TLS groupSelection details: all

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