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- PDB-3q0c: Crystal structure of SUVH5 SRA-fully methylated CG DNA complex in... -

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Basic information

Entry
Database: PDB / ID: 3q0c
TitleCrystal structure of SUVH5 SRA-fully methylated CG DNA complex in space group P6122
Components
  • DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*TP*T)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
KeywordsTRANSFERASE/DNA / SRA / fully methylated CG / SUVH5 / 5mC binding protein / Fully methylated CG DNA Duplex / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / epigenetic regulation of gene expression / methylation / 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. ...: / 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 motif / Pre-SET domain / 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 / SET domain superfamily / 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: 2.6567 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)43,7815
Polymers43,7564
Non-polymers241
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-8 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.462, 104.462, 176.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-12-

MG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21A
12X
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain X resid 362:376X0
211chain A and resid 362:376A362 - 376
112chain X resid 380:524X0
212chain A and resid 380:524A380 - 524

NCS ensembles :
ID
1
2

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


Mass: 3362.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically Synthesized
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 23% PEG 3350, 100 mM Bis-Trispropane, pH 7.0, 80 mM Mg-acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-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
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: 2.65→30 Å / Num. all: 17149 / Num. obs: 17149 / % possible obs: 100 % / Redundancy: 28.1 % / Rmerge(I) obs: 0.136 / Rsym value: 0.134 / Net I/σ(I): 27.1
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 28.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3 / Rsym value: 0.85 / % 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: PDB ENTRY 3Q0B

3q0b


Resolution: 2.6567→19.847 Å / SU ML: 0.98 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3034 862 5.06 %Random
Rwork0.2506 ---
all0.26 ---
obs0.2532 17028 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.098 Å2 / ksol: 0.276 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8556 Å2-0 Å20 Å2
2--1.8556 Å2-0 Å2
3----3.7113 Å2
Refinement stepCycle: LAST / Resolution: 2.6567→19.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 426 1 36 2706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062759
X-RAY DIFFRACTIONf_angle_d1.0213817
X-RAY DIFFRACTIONf_dihedral_angle_d19.9141056
X-RAY DIFFRACTIONf_chiral_restr0.056412
X-RAY DIFFRACTIONf_plane_restr0.006425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11X109X-RAY DIFFRACTIONPOSITIONAL0.024
12A109X-RAY DIFFRACTIONPOSITIONAL0.024
21X952X-RAY DIFFRACTIONPOSITIONAL0.029
22A952X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6567-2.82270.39441450.32442622X-RAY DIFFRACTION100
2.8227-3.03990.36061700.31352595X-RAY DIFFRACTION100
3.0399-3.34450.34941370.27612656X-RAY DIFFRACTION100
3.3445-3.82550.30041350.25542684X-RAY DIFFRACTION100
3.8255-4.80840.26411380.22192718X-RAY DIFFRACTION100
4.8084-19.84740.25431370.21882891X-RAY DIFFRACTION100

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