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- PDB-2mem: Solution NMR structure of SLED domain of Scml2 -

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Basic information

Entry
Database: PDB / ID: 2mem
TitleSolution NMR structure of SLED domain of Scml2
ComponentsSex comb on midleg-like protein 2
KeywordsTRANSCRIPTION / PRC1 / PcG
Function / homology
Function and homology information


PcG protein complex / anatomical structure morphogenesis / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleus
Similarity search - Function
SLED domain / Polycomb group protein, RNA binding region / RNA binding Region / : / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 ...SLED domain / Polycomb group protein, RNA binding region / RNA binding Region / : / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / : / mbt repeat / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Sex comb on midleg-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBezsonova, I.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Solution NMR Structure of the DNA-binding Domain from Scml2 (Sex Comb on Midleg-like 2).
Authors: Bezsonova, I.
History
DepositionSep 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sex comb on midleg-like protein 2


Theoretical massNumber of molelcules
Total (without water)13,1131
Polymers13,1131
Non-polymers00
Water00
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 Sex comb on midleg-like protein 2


Mass: 13112.892 Da / Num. of mol.: 1 / Fragment: UNP residues 354-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCML2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQR0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of SLED domain from Sex Comb on Midleg-like 2 (Scml2)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.3-1.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.3-1.0
Sample conditionsIonic strength: 250 / pH: 7.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
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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