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- PDB-2lxe: S4wyild -

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Basic information

Entry
Database: PDB / ID: 2lxe
TitleS4wyild
ComponentsHistone-lysine N-methyltransferase SUVR4
KeywordsTRANSFERASE / Ubiqutine binding domain / a-helical
Function / homology
Function and homology information


: / : / plasmodesma / Transferases; Transferring one-carbon groups; Methyltransferases / chromosome / nucleolus / zinc ion binding
Similarity search - Function
Histone-lysine N methyltransferase , C-terminal domain-like / WIYLD domain / Histone-lysine N-methyltransferase SUVR4/SUVR1/SUVR2 / WIYLD domain superfamily / Ubiquitin-binding WIYLD domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains ...Histone-lysine N methyltransferase , C-terminal domain-like / WIYLD domain / Histone-lysine N-methyltransferase SUVR4/SUVR1/SUVR2 / WIYLD domain superfamily / Ubiquitin-binding WIYLD domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SUVR4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKristiansen, P. / Rahman, M.A. / Aalen, R.B.
CitationJournal: Biochemistry / Year: 2014
Title: The arabidopsis histone methyltransferase SUVR4 binds ubiquitin via a domain with a four-helix bundle structure.
Authors: Rahman, M.A. / Kristiansen, P.E. / Veiseth, S.V. / Andersen, J.T. / Yap, K.L. / Zhou, M.M. / Sandlie, I. / Thorstensen, T. / Aalen, R.B.
History
DepositionAug 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SUVR4


Theoretical massNumber of molelcules
Total (without water)12,1651
Polymers12,1651
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone-lysine N-methyltransferase SUVR4 / Protein SET DOMAIN GROUP 31 / Suppressor of variegation 3-9-related protein 4 / Su(var)3-9-related protein 4


Mass: 12164.612 Da / Num. of mol.: 1 / Fragment: UNP residues 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUVR4, SDG31, SET31, At3g04380, T27C4.2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8W595, histone-lysine N-methyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
4212D 1H-15N HSQC
3312D 1H-15N HSQC
2412D 1H-15N HSQC
5512D 1H-15N HSQC
6612D 1H-15N HSQC
7712D 1H-15N HSQC
1813D 1H-13C NOESY
1923D CBCA(CO)NH
11023D C(CO)NH
11123D HNCO
11223D HNCA
11323D HN(CA)CB
11423D HN(CO)CA
11523D HBHA(CO)NH
11623D HN(CA)CO
11723D H(CCO)NH
11822D 1H-13C HSQC
11923D (H)CCH-TOCSY
12023D (H)CCH-COSY
12123D 1H-13C NOESY aliphatic
12223D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
195 % H2O, 5 % [U-100% 2H] D2O, 20 mM potassium phosphate, 0.2 mM DSS, 1.0 mM DTT, 50 mM sodium chloride, 0.8 mM [U-98% 15N] WYILD, 95% H2O/5% D2O95% H2O/5% D2O
295 % H2O, 5 % [U-100% 2H] D2O, 20 mM potassium phosphate, 0.2 mM DSS, 1.0 mM DTT, 50 mM sodium chloride, 0.8 mM [U-98% 13C; U-98% 15N] WYILD, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
95 %H2Onatural abundance1
5 %D2O[U-100% 2H]1
20 mMpotassium phosphatenatural abundance1
0.2 mMDSSnatural abundance1
1.0 mMDTTnatural abundance1
50 mMsodium chloridenatural abundance1
0.8 mMWYILD[U-98% 15N]1
95 %H2Onatural abundance2
5 %D2O[U-100% 2H]2
20 mMpotassium phosphatenatural abundance2
0.2 mMDSSnatural abundance2
1.0 mMDTTnatural abundance2
50 mMsodium chloridenatural abundance2
0.8 mMWYILD[U-98% 13C; U-98% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
170 6.5 ambient 298 K
270 6.5 ambient 308 K
370 6.5 ambient 303 K
470 6.5 ambient 313 K
570 6.5 ambient 293 K
670 6.5 ambient 288 K
770 6.5 ambient 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Herrmann, Guntert and Wuthrichstructure solution
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CARAKeller and Wuthrichdata analysis
TopSpinBruker Biospincollection
CYANA2Herrmann, Guntert and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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