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- PDB-6g99: Solution structure of FUS-ZnF bound to UGGUG -

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Basic information

Entry
Database: PDB / ID: 6g99
TitleSolution structure of FUS-ZnF bound to UGGUG
Components
  • RNA (5'-R(*UP*GP*GP*UP*G)-3')
  • RNA-binding protein FUS
KeywordsRNA BINDING PROTEIN / RNA zinc finger RNA binding protein zinc ribbon
Function / homology
Function and homology information


mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA-binding protein FUS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLoughlin, F.E. / Allain, F.H.-T.
CitationJournal: Mol. Cell / Year: 2019
Title: The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity.
Authors: Loughlin, F.E. / Lukavsky, P.J. / Kazeeva, T. / Reber, S. / Hock, E.M. / Colombo, M. / Von Schroetter, C. / Pauli, P. / Clery, A. / Muhlemann, O. / Polymenidou, M. / Ruepp, M.D. / Allain, F.H.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA-binding protein FUS
A: RNA (5'-R(*UP*GP*GP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1963
Polymers6,1312
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1110 Å2
ΔGint-4 kcal/mol
Surface area3830 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide RNA-binding protein FUS / / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 4528.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUS, TLS / Production host: Escherichia coli (E. coli) / References: UniProt: P35637
#2: RNA chain RNA (5'-R(*UP*GP*GP*UP*G)-3')


Mass: 1602.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-15N NOESY
134isotropic12D 1H-1H NOESY
142isotropic32D 13C F2-filtered NOESY
154isotropic22D 1H-13C HSQC aliphatic
164isotropic22D 1H-13C HSQC aromatic
NMR detailsText: NULL

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] FUS-ZnF, 1.0 mM RNA (5'-R(*UP*GP*GP*UP*G)-3'), 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 90% H2O/10% D2O13C_15N90% H2O/10% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] FUS-ZnF, 1.0 mM RNA (5'-R(*UP*GP*GP*UP*G)-3'), 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 100% D2O13C15N_D2O100% D2O
solution31.0 mM [U-99% 15N] FUS-ZnF, 0.9 mM RNA (5'-R(*UP*GP*GP*UP*G)-3'), 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 90% H2O/10% D2O15N_H2O90% H2O/10% D2O
solution41.0 mM [U-99% 13C; U-99% 15N] FUS-ZnF, 0.9 mM RNA (5'-R(*UP*GP*GP*UP*G)-3'), 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 100% D2O15N_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMFUS-ZnF[U-99% 13C; U-99% 15N]1
1.0 mMRNA (5'-R(*UP*GP*GP*UP*G)-3')natural abundance1
20 mMsodium phosphatenatural abundance1
1 mMbeta-mercaptoethanolnatural abundance1
0.8 mMFUS-ZnF[U-99% 13C; U-99% 15N]2
1.0 mMRNA (5'-R(*UP*GP*GP*UP*G)-3')natural abundance2
20 mMsodium phosphatenatural abundance2
1 mMbeta-mercaptoethanolnatural abundance2
1.0 mMFUS-ZnF[U-99% 15N]3
0.9 mMRNA (5'-R(*UP*GP*GP*UP*G)-3')natural abundance3
20 mMsodium phosphatenatural abundance3
1 mMbeta-mercaptoethanolnatural abundance3
1.0 mMFUS-ZnF[U-99% 13C; U-99% 15N]4
0.9 mMRNA (5'-R(*UP*GP*GP*UP*G)-3')natural abundance4
20 mMsodium phosphatenatural abundance4
1 mMbeta-mercaptoethanolnatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Temperature err
120 mM3036.5 AMBIENT Pa303 K0.5
220 mM2786.5 AMBIENT Pa278 K0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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