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- PDB-3q0b: Crystal structure of SUVH5 SRA- fully methylated CG DNA complex i... -

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Basic information

Entry
Database: PDB / ID: 3q0b
TitleCrystal structure of SUVH5 SRA- fully methylated CG DNA complex in space group P42212
Components
  • DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*T)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
KeywordsTRANSFERASE/DNA / SRA / fully methylated CG / SUVH5 / 5mC binding protein / Fully methylated CG duplex DNA / TRANSFERASE-DNA complex
Function / homology
Function and homology information


regulatory ncRNA-mediated heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / histone H3K9me2 methyltransferase activity / histone methyltransferase activity / chromosome, centromeric region / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / double-stranded DNA binding / 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 / MAD / Resolution: 2.2 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 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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: DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)21,6682
Polymers21,6682
Non-polymers00
Water1,13563
1
X: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
A: DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*T)-3')

X: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
A: DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)43,3364
Polymers43,3364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5150 Å2
ΔGint-8 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.566, 76.566, 73.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 / 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: 18609.711 Da / Num. of mol.: 1 / 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: pETSumo / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2 (DE3)
References: UniProt: O82175, histone-lysine N-methyltransferase
#2: DNA chain DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*T)-3')


Mass: 3058.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19% PEG 4000, 100 mM Tris-HCl, pH 7.5 and 40 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918,0.97929,0.9900
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: cryogenecally-cooled double crystal Si(111) monochromoter
RadiationMonochromator: Cryo-cooled Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979291
30.991
ReflectionResolution: 2.2→30 Å / Num. all: 11805 / Num. obs: 11770 / % possible obs: 99.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.047 / Rsym value: 0.051 / Net I/σ(I): 49.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.52 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→26.587 Å / SU ML: 0.59 / σ(F): 1.89 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1055 4.96 %Random
Rwork0.2167 ---
all0.22 11800 --
obs0.2184 11770 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.015 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0718 Å2-0 Å20 Å2
2---1.0718 Å2-0 Å2
3---2.1437 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 203 0 63 1402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071383
X-RAY DIFFRACTIONf_angle_d1.1981911
X-RAY DIFFRACTIONf_dihedral_angle_d19.052528
X-RAY DIFFRACTIONf_chiral_restr0.065206
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30010.36321450.29522498X-RAY DIFFRACTION99
2.3001-2.42130.29371300.24642539X-RAY DIFFRACTION100
2.4213-2.57290.31381420.23432513X-RAY DIFFRACTION100
2.5729-2.77130.2551330.23662532X-RAY DIFFRACTION100
2.7713-3.04990.34171120.2422561X-RAY DIFFRACTION100
3.0499-3.49040.23421460.2112504X-RAY DIFFRACTION100
3.4904-4.39430.21981260.1782532X-RAY DIFFRACTION100
4.3943-26.5890.20131210.19782515X-RAY DIFFRACTION99

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