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- PDB-5w3n: Molecular structure of FUS low sequence complexity domain protein... -

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Basic information

Entry
Database: PDB / ID: 5w3n
TitleMolecular structure of FUS low sequence complexity domain protein fibrils
ComponentsRNA-binding protein FUS
KeywordsPROTEIN FIBRIL / Low complexity sequence domain / RNA transport / RNA Granule / intrinsically disordered protein
Function / homology
Function and homology information


mRNA stabilization / positive regulation of double-strand break repair via homologous recombination / intracellular non-membrane-bounded organelle / 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 / positive regulation of double-strand break repair via homologous recombination / intracellular non-membrane-bounded organelle / 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 / 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-binding protein FUS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsMurray, D.T. / Kato, M. / Lin, Y. / Thurber, K. / Hung, I. / McKnight, S. / Tycko, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5U01GM107623-03 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1FI2GM117604-01 United States
CitationJournal: Cell / Year: 2017
Title: Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains.
Authors: Murray, D.T. / Kato, M. / Lin, Y. / Thurber, K.R. / Hung, I. / McKnight, S.L. / Tycko, R.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _citation_author.name / _pdbx_nmr_software.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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
Revision 1.5May 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

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein FUS
B: RNA-binding protein FUS
C: RNA-binding protein FUS
D: RNA-binding protein FUS
E: RNA-binding protein FUS
F: RNA-binding protein FUS
G: RNA-binding protein FUS
H: RNA-binding protein FUS
I: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)223,8299
Polymers223,8299
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Mass-per-length measurements were performed on a transmission electron microscope to determine the repeating unit in the protein fibril. Atomic force microscopy images support ...Evidence: microscopy, Mass-per-length measurements were performed on a transmission electron microscope to determine the repeating unit in the protein fibril. Atomic force microscopy images support the diameter of the calculated macromolecular assembly.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35890 Å2
ΔGint-48 kcal/mol
Surface area17380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 4928structures with no violations, lowest energy, and derived from one of 44 independent calculations
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: 24869.846 Da / Num. of mol.: 9 / Fragment: UNP residues 2-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUS, TLS
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P35637

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D NCACX
121isotropic13D NCOCX
131isotropic33D CONCA
141isotropic33D CANCX
154isotropic413C-13C PITHIRDS-CT
165isotropic413C-13C PITHIRDS-CT
171isotropic215N-15N BARE
182isotropic215N-15N BARE
192isotropic213C-13C DARR
1103isotropic213C-13C DARR
1112isotropic13D NCACX
1123isotropic13D NCOCX

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid10.28 mg/uL [U-99% 13C; U-99% 15N] FUS-LC Fibril, 100% H2OUniformly 15N,13C labeled FUS low sequence complexity domain protein fibrilsU-FUS-LC100% H2O
solid20.28 mg/uL 99% 15N, 99% 2-13C Glycerol FUS-LC Fibril, 100% H2OUniformly 15N, 2-13C glycerol labeled FUS low sequence complexity domain protein fibrils2-Glc-FUS-LC100% H2O
solid30.28 mg/uL 99% 15N, 99% 1,3-13C Glycerol FUS-LC Fibril, 100% H2OUniformly 15N, 1,3-13C glycerol labeled FUS low sequence complexity domain protein fibrils1,3-Glc-FUS-LC100% H2O
solid40.23 mg/uL 99% 1-13C Tyrosine FUS-LC Fibril, 100% H2O1-13C Tyrosine labeled FUS low sequence complexity domain fibrils1-13C-Tyr-FUS-LC100% H2O
solid50.23 mg/uL 99% 1-13C Threonine FUS-LC Fibril, 100% H2O1-13C Threonine labeled FUS low sequence complexity domain fibrils1-13C-Thr-FUS-LC100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.28 mg/uLFUS-LC Fibril[U-99% 13C; U-99% 15N]1
0.28 mg/uLFUS-LC Fibril99% 15N, 99% 2-13C Glycerol2
0.28 mg/uLFUS-LC Fibril99% 15N, 99% 1,3-13C Glycerol3
0.23 mg/uLFUS-LC Fibril99% 1-13C Tyrosine4
0.23 mg/uLFUS-LC Fibril99% 1-13C Threonine5
Sample conditionsDetails: Samples are hydrated protein fibrils in 20 mM sodium phosphate, pH 7.4
Ionic strength: 20 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III895.11
Varian InfinityVarianInfinity746.12
Varian InfinityPlusVarianInfinityPlus599.23
Bruker AVANCE IIIBrukerAVANCE III400.64

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Processing

NMR software
NameVersionDeveloperClassification
MCASSIGN2BKan-Nian Hu, Wei Qiang, and Robert Tyckochemical shift assignment
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLOR NIH2.45Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
Details: Calculate 448 initial folds for an extended FUS monomer with nine identical copies. Select 10% lowest energy for further calculations. Calculate 112 structures for each lowest energy model ...Details: Calculate 448 initial folds for an extended FUS monomer with nine identical copies. Select 10% lowest energy for further calculations. Calculate 112 structures for each lowest energy model in first round of calculations. Analyze 10% lowest energy structures in each run and select based on stated selection criterion.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with no violations, lowest energy, and derived from one of 44 independent calculations
Conformers calculated total number: 4928 / Conformers submitted total number: 20

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