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- PDB-3q0f: Crystal structure of SUVH5 SRA- methylated CHH DNA complex -

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Basic information

Entry
Database: PDB / ID: 3q0f
TitleCrystal structure of SUVH5 SRA- methylated CHH DNA complex
Components
  • DNA (5'-D(*CP*TP*GP*AP*GP*GP*AP*GP*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*CP*TP*(5CM)P*CP*TP*CP*AP*G)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
KeywordsTRANSFERASE/DNA / SRA / fully methylated CG / SUVH5 / 5mC binding domain / Methylated CHH 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 / DNA (> 10) / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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 1.4Apr 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(*CP*TP*GP*AP*GP*GP*AP*GP*TP*AP*T)-3')
C: DNA (5'-D(*TP*AP*CP*TP*(5CM)P*CP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)43,4394
Polymers43,4394
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-17 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.968, 102.968, 170.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain X resid 362:399
211chain A and resid 362:399
112chain X resid 405:414
212chain A and resid 405:414
113chain X resid 424:524
213chain A and resid 424:524

NCS ensembles :
ID
1
2
3

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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: 18515.920 Da / Num. of mol.: 2 / Fragment: SUVH5 SRA Domain (UNP Residues 362-528)
Source method: isolated from a genetically manipulated source
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(*CP*TP*GP*AP*GP*GP*AP*GP*TP*AP*T)-3')


Mass: 3413.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized
#3: DNA chain DNA (5'-D(*TP*AP*CP*TP*(5CM)P*CP*TP*CP*AP*G)-3')


Mass: 2993.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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 Å3/Da / Density % sol: 59.04 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG4000, 100 mM Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 14607 / Num. obs: 14578 / % possible obs: 99.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.088 / Net I/σ(I): 26
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 100

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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 P42212 space group

Resolution: 2.75→29.283 Å / SU ML: 1.09 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 729 5.04 %Random
Rwork0.2294 ---
obs0.2315 14466 99.69 %-
all-14500 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.6 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7339 Å2-0 Å2-0 Å2
2--7.7339 Å20 Å2
3----15.4678 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 425 0 18 2682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072757
X-RAY DIFFRACTIONf_angle_d1.2943817
X-RAY DIFFRACTIONf_dihedral_angle_d20.9051040
X-RAY DIFFRACTIONf_chiral_restr0.071415
X-RAY DIFFRACTIONf_plane_restr0.006425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11X300X-RAY DIFFRACTIONPOSITIONAL
12A300X-RAY DIFFRACTIONPOSITIONAL0.026
21X64X-RAY DIFFRACTIONPOSITIONAL
22A64X-RAY DIFFRACTIONPOSITIONAL0.03
31X645X-RAY DIFFRACTIONPOSITIONAL
32A645X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.96220.33531490.29572655X-RAY DIFFRACTION100
2.9622-3.25990.33491550.25552679X-RAY DIFFRACTION100
3.2599-3.73080.23841250.21612734X-RAY DIFFRACTION100
3.7308-4.69730.2321520.18712763X-RAY DIFFRACTION100
4.6973-29.28420.27981480.23512906X-RAY DIFFRACTION99

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