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- PDB-6a5m: Crystal structure of Arabidopsis thaliana SUVH6 in complex with S... -

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Basic information

Entry
Database: PDB / ID: 6a5m
TitleCrystal structure of Arabidopsis thaliana SUVH6 in complex with SAM, form 2
ComponentsHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6Histone methyltransferase
KeywordsGENE REGULATION / SRA / SET / histone methyltransferase / DNA methylation
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 / 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 domain / Pre-SET motif / Pre-SET domain profile. ...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 domain / Pre-SET motif / 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 superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0976
Polymers59,4371
Non-polymers6605
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.546, 77.098, 66.820
Angle α, β, γ (deg.)90.00, 110.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6 / Histone methyltransferase / 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: 59437.230 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M di-Sodium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24000 / % possible obs: 98.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1223 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5K
Resolution: 2.301→38.549 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 1223 5.1 %
Rwork0.1778 --
obs0.1801 23963 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→38.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 31 193 4078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073960
X-RAY DIFFRACTIONf_angle_d1.1235338
X-RAY DIFFRACTIONf_dihedral_angle_d16.3931510
X-RAY DIFFRACTIONf_chiral_restr0.042569
X-RAY DIFFRACTIONf_plane_restr0.005694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3008-2.39290.27941190.20532444X-RAY DIFFRACTION96
2.3929-2.50180.27031340.22032508X-RAY DIFFRACTION98
2.5018-2.63370.28891440.21012508X-RAY DIFFRACTION99
2.6337-2.79870.25511360.20272519X-RAY DIFFRACTION99
2.7987-3.01470.27041330.20322539X-RAY DIFFRACTION99
3.0147-3.31790.29241340.19462528X-RAY DIFFRACTION99
3.3179-3.79770.20521380.1692533X-RAY DIFFRACTION99
3.7977-4.78320.17261430.14342580X-RAY DIFFRACTION99
4.7832-38.55440.17961420.16432581X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3717-1.62670.01043.6173-0.50280.8705-0.0138-0.1198-0.19720.0483-0.03170.3681-0.0337-0.13440.08610.2235-0.01560.03310.34440.00080.2686-30.20228.6814-11.6385
24.4115-1.33640.82872.8801-0.84492.14450.0680.30210.0714-0.1007-0.0595-0.0977-0.2007-0.0027-0.06660.31640.0120.04950.28490.00990.2515-29.467328.2295-20.7725
31.5474-0.69290.13371.4457-0.11310.47540.14530.23640.212-0.1944-0.216-0.41270.03240.16330.08610.318-0.00710.05370.33490.02230.2566-4.475413.8489-19.9962
43.26811.93411.17321.3150.12043.26820.44440.643-0.8928-0.75580.20590.50730.4521-0.7780.04190.6248-0.0214-0.12690.522-0.11660.6575-16.7238-20.4801-22.2729
51.72290.74250.28252.54510.41170.96570.07670.235-0.0611-0.1926-0.0852-0.03070.0080.0178-0.01360.22920.02760.01240.26090.00460.2013-8.6677-2.1279-16.8198
62.4813-0.462-0.90344.1435-0.33642.61410.0663-1.2666-0.19280.3251-0.0551-0.52350.10360.3290.01750.4556-0.0146-0.02510.3593-0.00580.2926-2.8565-5.4586-1.2992
71.9159-0.87570.14122.7841.18651.60310.0194-0.06390.09820.3690.0389-0.30950.18510.0854-0.07780.2884-0.0247-0.0090.2750.02450.2679-2.82042.6177-2.9704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 267 through 367 )
2X-RAY DIFFRACTION2chain 'A' and (resid 368 through 468 )
3X-RAY DIFFRACTION3chain 'A' and (resid 469 through 550 )
4X-RAY DIFFRACTION4chain 'A' and (resid 551 through 572 )
5X-RAY DIFFRACTION5chain 'A' and (resid 573 through 647 )
6X-RAY DIFFRACTION6chain 'A' and (resid 648 through 705 )
7X-RAY DIFFRACTION7chain 'A' and (resid 706 through 790 )

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