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- PDB-6n3g: Crystal structure of histone lysine methyltransferase SmyD2 in co... -

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Basic information

Entry
Database: PDB / ID: 6n3g
TitleCrystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene glycol
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE / Methyltransferase / Complex
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 / regulation of DNA damage response, signal transduction by p53 class mediator / histone H3 methyltransferase activity / 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 / regulation of DNA damage response, signal transduction by p53 class mediator / histone H3 methyltransferase activity / 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 / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
SMYD2, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / 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 signature. / Zinc finger, MYND-type / 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 / SET domain superfamily / 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
ETHANOL / NICKEL (II) ION / S-ADENOSYL-L-HOMOCYSTEINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsPerry, E. / Spellmon, N. / Brunzelle, J. / Yang, Z.
CitationJournal: To be Published
Title: Crystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene glycol
Authors: Perry, E. / Yang, Z.
History
DepositionNov 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,30713
Polymers49,8321
Non-polymers1,47512
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-1 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.840, 151.840, 53.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 1 molecules A

#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 BL21(DE3) (bacteria)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 6 types, 91 molecules

#2: 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
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Ethanol, Water, 1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.43→107.367 Å / Num. obs: 14389 / % possible obs: 94.8 % / Redundancy: 14.2 % / CC1/2: 0.993 / Rpim(I) all: 0.096 / Net I/σ(I): 10.3
Reflection shellResolution: 2.43→2.718 Å / Num. unique obs: 718 / CC1/2: 0.559 / Rpim(I) all: 0.538 / % possible all: 72.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
XDSVERSION Jun 1, 2017 BUILT=20170923data reduction
Aimless0.6.2data scaling
PHENIX1.11.1-2575phasing
autoPROC1.0.5 (20171219)data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KJK

5kjk


Resolution: 2.43→75.92 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.38
RfactorNum. reflection% reflection
Rfree0.2224 753 5.24 %
Rwork0.1747 --
obs0.1772 14382 61.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.26 Å2 / Biso mean: 37.8088 Å2 / Biso min: 13.25 Å2
Refinement stepCycle: final / Resolution: 2.43→75.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 83 79 3624
Biso mean--39.43 34.82 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113625
X-RAY DIFFRACTIONf_angle_d1.3134868
X-RAY DIFFRACTIONf_chiral_restr0.075513
X-RAY DIFFRACTIONf_plane_restr0.012623
X-RAY DIFFRACTIONf_dihedral_angle_d22.4252209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4302-2.61780.373240.30943203447
2.6178-2.88130.2816670.27941111117825
2.8813-3.29820.28621770.24263224340173
3.2982-4.15540.23852480.170144244672100
4.1554-75.9570.17282370.140945504787100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9662-0.27370.93730.6147-0.28062.3062-0.00650.0702-0.014-0.0157-0.00170.33940.2741-0.1836-0.05350.21290.0316-0.10080.1701-0.0270.2681157.581750.1216-6.384
21.07710.29060.17270.93410.06091.9642-0.0839-0.15040.07870.04380.1473-0.00590.21450.1942-0.02620.18920.0987-0.0370.1486-0.03850.1622170.554249.71640.2415
36.6266-0.46841.84372.2629-0.72782.7672-0.0183-0.14390.19070.16420.0923-0.1539-0.15420.39820.12090.1416-0.0146-0.11030.2181-0.1440.2988180.837761.32890.4948
42.36140.2440.8182.22930.08824.2684-0.18630.08050.709-0.1434-0.0285-0.4015-0.90350.78840.18520.4296-0.06820.01270.314-0.01230.5807192.235861.2582-13.5541
51.35140.30190.24691.68941.07052.49930.01530.41610.2859-0.21050.052-0.1616-0.10030.76420.0090.18350.1029-0.00190.45860.06740.2394187.73649.3019-19.4788
65.0571-1.0209-2.21860.42550.0412.4003-0.35480.0365-0.6967-0.0309-0.0010.13910.95530.04980.27760.46990.11330.00660.2382-0.07280.2218180.792631.5925-10.9431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 168 )A4 - 168
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 246 )A169 - 246
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 269 )A247 - 269
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 310 )A270 - 310
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 378 )A311 - 378
6X-RAY DIFFRACTION6chain 'A' and (resid 379 through 433 )A379 - 433

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