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- PDB-3q0d: Crystal structure of SUVH5 SRA- hemi methylated CG DNA complex -

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Basic information

Entry
Database: PDB / ID: 3q0d
TitleCrystal structure of SUVH5 SRA- hemi methylated CG DNA complex
Components
  • DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*AP*(5CM)P*GP*TP*CP*AP*G)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5Histone methyltransferase
KeywordsTRANSFERASE/DNA / SRA / hemi-methylated CG / SUVH5 / 5mC binding / Hemi-methylated CG DNA / TRANSFERASE-DNA complex
Function / homology
Function and homology information


: / [histone H3]-lysine9 N-methyltransferase / regulatory ncRNA-mediated heterochromatin formation / histone H3K9me2 methyltransferase activity / histone methyltransferase activity / chromosome, centromeric region / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / zinc ion binding / nucleus
Similarity search - Function
Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / PUA domain-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain ...Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / PUA domain-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / PUA-like superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3704 Å
AuthorsEerappa, R. / Simanshu, D.K. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2011
Title: A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo.
Authors: Rajakumara, E. / Law, J.A. / Simanshu, D.K. / Voigt, P. / Johnson, L.M. / Reinberg, D. / Patel, D.J. / Jacobsen, S.E.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 27, 2013Group: Advisory
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
B: DNA (5'-D(*TP*CP*CP*AP*(5CM)P*GP*TP*CP*AP*G)-3')
C: DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1715
Polymers43,1364
Non-polymers351
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-18 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.379, 76.379, 74.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain X and (resseq 362:399 or resseq 405:435 or resseq...
211chain A and (resseq 362:399 or resseq 405:435 or resseq...

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 / Histone methyltransferase / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Protein SET DOMAIN GROUP 9 / Suppressor of ...Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Protein SET DOMAIN GROUP 9 / Suppressor of variegation 3-9 homolog protein 5 / Su(var)3-9 homolog protein 5


Mass: 18515.920 Da / Num. of mol.: 2 / Fragment: SUVH5 SRA Domain (UNP Residues 362-528)
Source method: isolated from a genetically manipulated source
Details: Cleavable N-terminal His-SUmo tag / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g35160, SDG9, SET9, SUVH5, T4C15.17 / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: O82175, histone-lysine N-methyltransferase
#2: DNA chain DNA (5'-D(*TP*CP*CP*AP*(5CM)P*GP*TP*CP*AP*G)-3')


Mass: 3019.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: DNA chain DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*GP*A)-3')


Mass: 3085.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 19% PEG4000, 100 mM MES, pH 6.5, 200 mM NaCl and 3 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: Cryogenecally-cooled double Si(111) monochromoter
RadiationMonochromator: Cryo-cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.37→20 Å / Num. all: 17443 / Num. obs: 17234 / % possible obs: 98.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.068 / Net I/σ(I): 30.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPMRphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SRA Molecule from the SUVH5 SRA-fully methylated Cg DNA crystallized in space group P42212

Resolution: 2.3704→19.095 Å / SU ML: 0.35 / σ(F): 1.39 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 873 5.07 %
Rwork0.2246 --
obs0.2265 17221 98.78 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.199 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8426 Å2-0 Å20 Å2
2--1.8426 Å20 Å2
3----7.7466 Å2
Refinement stepCycle: LAST / Resolution: 2.3704→19.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 405 1 51 2630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093114
X-RAY DIFFRACTIONf_angle_d1.3784382
X-RAY DIFFRACTIONf_dihedral_angle_d22.4581195
X-RAY DIFFRACTIONf_chiral_restr0.082486
X-RAY DIFFRACTIONf_plane_restr0.007433
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11X966X-RAY DIFFRACTIONPOSITIONAL
12A966X-RAY DIFFRACTIONPOSITIONAL0.031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3704-2.51860.33091350.30622584X-RAY DIFFRACTION94
2.5186-2.71250.31711320.26312737X-RAY DIFFRACTION100
2.7125-2.98460.31621460.2762758X-RAY DIFFRACTION100
2.9846-3.41430.30281420.25312751X-RAY DIFFRACTION100
3.4143-4.29360.26681700.21412738X-RAY DIFFRACTION100
4.2936-19.09540.21241480.19332780X-RAY DIFFRACTION99

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