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- PDB-6gbm: Solution structure of FUS-RRM bound to stem-loop RNA -

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Basic information

Entry
Database: PDB / ID: 6gbm
TitleSolution structure of FUS-RRM bound to stem-loop RNA
Components
  • RNA (5'-R(*GP*GP*CP*AP*GP*AP*UP*UP*AP*CP*AP*AP*UP*UP*CP*UP*AP*UP*UP*UP*GP*CP*C)-3')
  • RNA-binding protein FUS
KeywordsRNA BINDING PROTEIN / RNA / RNA recognition motif / RRM
Function / homology
Function and homology information


mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / 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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...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 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / 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 15, 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

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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(*GP*GP*CP*AP*GP*AP*UP*UP*AP*CP*AP*AP*UP*UP*CP*UP*AP*UP*UP*UP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,5762
Polymers18,5762
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2240 Å2
ΔGint-14 kcal/mol
Surface area9490 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 RNA-binding protein FUS / / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 11289.521 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(*GP*GP*CP*AP*GP*AP*UP*UP*AP*CP*AP*AP*UP*UP*CP*UP*AP*UP*UP*UP*GP*CP*C)-3')


Mass: 7286.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY aromatic
121isotropic13D 1H-15N NOESY
131isotropic23D 1H-13C NOESY aliphatic
144isotropic13D 1H-13C NOESY aliphatic
154isotropic23D 1H-13C NOESY aromatic
165isotropic12D 1H-1H NOESY
173isotropic22D 1H-15N HSQC
181isotropic12D 1H-15N HSQC
192isotropic22D 1H-13C HSQC
1104isotropic12D 1H-13C HSQC
NMR detailsText: NULL

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] FUS-RRM, 0.8 mM [U-99% 15N] RNA stem loop, 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 90% H2O/10% D2O13C15NRRM_SL_H2O90% H2O/10% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] FUS-RRM, 0.8 mM [U-99% 15N] stem-loop RNA, 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 100% D2O13C15NRRM_SL_D2O100% D2O
solution31 mM [U-99% 15N] FUS-RRM, 0.8 mM [U-99% 13C; U-99% 15N] stem-loop RNA, 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 90% H2O/10% D2O13C15NRNA_RRM_H2O90% H2O/10% D2O
solution41.0 mM [U-99% 15N] FUS-RRM, 0.8 mM [U-99% 13C; U-99% 15N] stem-loop RNA, 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 100% D2O13C15NRNA_RRM_D2O100% D2O
solution51.0 mM [U-99% 15N] FUS-RRM, 1.0 mM [U-99% 15N] stem-loop RNA, 20 mM sodium phosphate, 1 mM beta-mercaptoethanol, 100% D2O15NRRM_SL_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMFUS-RRM[U-99% 13C; U-99% 15N]1
0.8 mMRNA stem loop[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
1 mMbeta-mercaptoethanolnatural abundance1
0.8 mMFUS-RRM[U-99% 13C; U-99% 15N]2
0.8 mMstem-loop RNA[U-99% 15N]2
20 mMsodium phosphatenatural abundance2
1 mMbeta-mercaptoethanolnatural abundance2
1 mMFUS-RRM[U-99% 15N]3
0.8 mMstem-loop RNA[U-99% 13C; U-99% 15N]3
20 mMsodium phosphatenatural abundance3
1 mMbeta-mercaptoethanolnatural abundance3
1.0 mMFUS-RRM[U-99% 15N]4
0.8 mMstem-loop RNA[U-99% 13C; U-99% 15N]4
20 mMsodium phosphatenatural abundance4
1 mMbeta-mercaptoethanolnatural abundance4
1.0 mMFUS-RRM[U-99% 15N]5
1.0 mMstem-loop RNA[U-99% 15N]5
20 mMsodium phosphatenatural abundance5
1 mMbeta-mercaptoethanolnatural abundance5
Sample conditionsIonic strength: 20 mM / Label: 303K / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker AvanceIIIBrukerAvanceIII7002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddarddata analysis
CANDIDHerrmann, Guntert and Wuthrichpeak picking
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
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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