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- PDB-6a5n: Crystal structure of Arabidopsis thaliana SUVH6 in complex with m... -

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Basic information

Entry
Database: PDB / ID: 6a5n
TitleCrystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA
Components
  • DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3')
  • DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)-3')
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
KeywordsGENE REGULATION/DNA / SRA / SET / histone methyltransferase / DNA methylation / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


methyl-CpNpG binding / methyl-CpNpN binding / [histone H3]-lysine9 N-methyltransferase / histone H3K9me2 methyltransferase activity / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / 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 / 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 ...: / Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / 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 / Beta-clip-like / SET domain / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0503200 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.
Authors: Li, X. / Harris, C.J. / Zhong, Z. / Chen, W. / Liu, R. / Jia, B. / Wang, Z. / Li, S. / Jacobsen, S.E. / Du, J.
History
DepositionJun 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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_conn_type
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
C: DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)-3')
D: DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8336
Polymers67,6373
Non-polymers1963
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-12 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.137, 79.443, 107.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6 / Histone H3-K9 methyltransferase 6 / H3-K9-HMTase 6 / Protein SET DOMAIN GROUP 23 / Suppressor of ...Histone H3-K9 methyltransferase 6 / H3-K9-HMTase 6 / Protein SET DOMAIN GROUP 23 / Suppressor of variegation 3-9 homolog protein 6 / Su(var)3-9 homolog protein 6


Mass: 59062.066 Da / Num. of mol.: 1 / Mutation: P777L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUVH6, SDG23, SET23, At2g22740, T9I22.18 / Plasmid: pET-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: Q8VZ17, histone-lysine N-methyltransferase
#2: DNA chain DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)-3')


Mass: 4318.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: methylated DNA / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3')


Mass: 4255.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: complementary DNA / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% ethanol, 10% w/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25062 / % possible obs: 97.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 32.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2497 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5K

6a5k


Resolution: 2.4→33.592 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.83
RfactorNum. reflection% reflection
Rfree0.2794 1267 5.09 %
Rwork0.2304 --
obs0.2332 24873 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 534 3 40 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094615
X-RAY DIFFRACTIONf_angle_d1.3146331
X-RAY DIFFRACTIONf_dihedral_angle_d22.0341784
X-RAY DIFFRACTIONf_chiral_restr0.077678
X-RAY DIFFRACTIONf_plane_restr0.005737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.37531170.31292615X-RAY DIFFRACTION99
2.4962-2.60970.38791360.31782633X-RAY DIFFRACTION100
2.6097-2.74730.47551290.38382602X-RAY DIFFRACTION96
2.7473-2.91930.35041520.28642640X-RAY DIFFRACTION100
2.9193-3.14450.31581420.27292641X-RAY DIFFRACTION100
3.1445-3.46070.30781600.25322674X-RAY DIFFRACTION99
3.4607-3.96080.29461260.23462434X-RAY DIFFRACTION90
3.9608-4.98760.2271660.18112632X-RAY DIFFRACTION97
4.9876-33.59490.22771390.18732735X-RAY DIFFRACTION96
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)
16.018-2.25090.04081.41210.48291.2209-0.046-0.1152-0.4590.10120.06350.16340.1304-0.1417-0.00060.3304-0.01740.03880.38120.0990.3914-29.9449-1.433104.8948
25.1903-2.2419-3.65210.82961.5912.8406-0.6438-0.6115-0.53310.67260.2150.18520.78060.08810.47920.71080.13760.03440.59140.11980.6337-30.7228-6.837124.8953
31.6902-0.55450.08651.9706-0.32341.7011-0.1245-0.38490.25330.16370.04880.1655-0.1628-0.05770.06810.33630.04190.06450.6223-0.00910.5026-51.22114.4849123.4487
48.66760.8839-0.93635.87460.02755.88630.10880.99680.2007-0.759-0.05660.39160.4391-1.0897-0.09870.53150.036-0.0050.42510.0930.718-36.3662-9.407493.1175
58.88855.4794-5.39344.602-4.47154.4422-0.67210.2138-2.1893-1.9563-0.1656-0.51571.80011.70040.93581.3401-0.00120.2750.75090.0370.9317-41.7594-16.649397.49
64.5975.48432.47269.35640.36193.89330.15451.1694-0.41361.18640.73370.23240.13030.7509-0.43651.06770.16150.31151.08340.1680.7921-26.6718-1.497389.0387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 469 )
2X-RAY DIFFRACTION2chain 'A' and (resid 470 through 518 )
3X-RAY DIFFRACTION3chain 'A' and (resid 519 through 780 )
4X-RAY DIFFRACTION4chain 'C' and (resid 2 through 14 )
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 8 )
6X-RAY DIFFRACTION6chain 'D' and (resid 9 through 14 )

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