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- PDB-2w0t: Solution structure of the FCS zinc finger domain of human LMBL2 -

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Basic information

Entry
Database: PDB / ID: 2w0t
TitleSolution structure of the FCS zinc finger domain of human LMBL2
ComponentsLETHAL(3)MALIGNANT BRAIN TUMOR-LIKE 2 PROTEIN
KeywordsTRANSCRIPTION / ZINC / YACG / LMBL2 / NUCLEUS / ZINC-FINGER / RNA BINDING / MBT REPEATS / PCG PROTEINS / POLYMORPHISM / MYM ZINC FINGER / TREBLE CLEF FOLD / CHROMATIN REGULATOR / HUMAN LETHAL(3) MALIGNANT BRAIN TUMOR 2 PROTEIN / ALTERNATIVE SPLICING / TRANSCRIPTION REGULATION / METAL-BINDING / PHOSPHOPROTEIN / POLYCOMB GROUP
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / methylated histone binding / SUMOylation of chromatin organization proteins / chromatin organization / histone binding / negative regulation of DNA-templated transcription / chromatin binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #160 / : / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #160 / : / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lethal(3)malignant brain tumor-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR
AuthorsLechtenberg, B.C. / Allen, M.D. / Bycroft, M.
CitationJournal: Protein Sci. / Year: 2009
Title: Solution Structure of the Fcs Zinc Finger Domain of the Human Polycomb Group Protein L(3)Mbt-Like 2.
Authors: Lechtenberg, B.C. / Allen, M.D. / Rutherford, T.J. / Freund, S.M. / Bycroft, M.
History
DepositionOct 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE 2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6732
Polymers4,6071
Non-polymers651
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 / 20
RepresentativeModel #1

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Components

#1: Protein/peptide LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE 2 PROTEIN / L(3)MBT-LIKE 2 PROTEIN / H-L(3)MBT-LIKE PROTEIN


Mass: 4607.234 Da / Num. of mol.: 1 / Fragment: FCS ZINC FINGER DOMAIN, RESIDUES 82-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q969R5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
14113C- CTHSCQ
1511H-15N-HSQC
161HNCO
171HN(CA)CB
181CACBCOHN
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/ 10% D2O
Sample conditionsIonic strength: 400 mM / pH: 6.3 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAvance8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
SPARKYstructure solution
CNSstructure solution
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 20

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