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- PDB-5whn: Crystal structure of the segment, NFGAFS, from the low complexity... -

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Basic information

Entry
Database: PDB / ID: 5whn
TitleCrystal structure of the segment, NFGAFS, from the low complexity domain of TDP-43, residues 312-317
ComponentsSegment of TAR DNA-binding protein 43
KeywordsPROTEIN FIBRIL / Amyloid / LARKS / TDP-43
Function / homology
Function and homology information


nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular membraneless organelle / negative regulation of protein phosphorylation / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular membraneless organelle / negative regulation of protein phosphorylation / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing / response to endoplasmic reticulum stress / mRNA 3'-UTR binding / molecular condensate scaffold activity / positive regulation of insulin secretion / regulation of circadian rhythm / regulation of protein stability / positive regulation of protein import into nucleus / mRNA processing / cytoplasmic stress granule / rhythmic process / regulation of gene expression / double-stranded DNA binding / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / chromatin / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
TAR DNA-binding protein 43, N-terminal / : / TAR DNA-binding protein 43, N-terminal domain / TAR DNA-binding protein 43, C-terminal / 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
TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsGuenther, E.L. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)NIH NIA AG029430 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.
Authors: Elizabeth L Guenther / Qin Cao / Hamilton Trinh / Jiahui Lu / Michael R Sawaya / Duilio Cascio / David R Boyer / Jose A Rodriguez / Michael P Hughes / David S Eisenberg /
Abstract: The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is ...The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation.
History
DepositionJul 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segment of TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)6421
Polymers6421
Non-polymers00
Water00
1
A: Segment of TAR DNA-binding protein 43
x 15


Theoretical massNumber of molelcules
Total (without water)9,62515
Polymers9,62515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
crystal symmetry operation4_435x-1/2,-y-3/2,-z1
crystal symmetry operation4_465x-1/2,-y+3/2,-z1
crystal symmetry operation4_425x-1/2,-y-5/2,-z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation4_535x+1/2,-y-3/2,-z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
crystal symmetry operation4_525x+1/2,-y-5/2,-z1
Unit cell
Length a, b, c (Å)13.820, 4.850, 46.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Segment of TAR DNA-binding protein 43 / TDP-43


Mass: 641.673 Da / Num. of mol.: 1 / Fragment: UNP residues 312-317 / Source method: obtained synthetically
Details: Synthetic peptide NFGAFS corresponding tosegment 312-317 of TDP-43
Source: (synth.) Homo sapiens (human) / References: UniProt: Q13148

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100mM phosphate/citrate 4.2, 40% ethanol, 5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→13.253 Å / Num. obs: 1447 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 8.299 % / Biso Wilson estimate: 4.49 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.184 / Χ2: 0.955 / Net I/σ(I): 9.65 / Num. measured all: 12008 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.146.3740.7262.521230.8230.78975.9
1.14-1.197.5350.5173.851420.9090.55390.4
1.19-1.249.6810.4236.021190.9410.44883.8
1.24-1.39.3470.3597.061240.9630.383100
1.3-1.379.3760.3327.471250.9580.35299.2
1.37-1.458.9610.2848.661270.9350.303100
1.45-1.557.9210.2038.981270.9880.21898.4
1.55-1.688.1670.18210.781080.9830.19694.7
1.68-1.848.8790.15313.69910.9640.16497.8
1.84-2.069.0430.11914.98920.9930.127100
2.06-2.387.9390.11216.29990.990.12100
2.38-2.917.2290.09716.97700.9920.10698.6
2.91-4.117.9680.09318.55620.9960.099100
4.11-13.2535.7630.09415.95380.9890.10392.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXdev_1555refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DGJ

3dgj


Resolution: 1.1→13.253 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.3
RfactorNum. reflection% reflection
Rfree0.1601 145 10.03 %
Rwork0.1334 --
obs0.136 1445 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 8.39 Å2 / Biso mean: 4.55 Å2 / Biso min: 3.06 Å2
Refinement stepCycle: final / Resolution: 1.1→13.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46 0 0 0 46
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652
X-RAY DIFFRACTIONf_angle_d0.9570
X-RAY DIFFRACTIONf_chiral_restr0.16
X-RAY DIFFRACTIONf_plane_restr0.00510
X-RAY DIFFRACTIONf_dihedral_angle_d12.68216
LS refinement shellResolution: 1.0995→13.2538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1601 145 -
Rwork0.1334 1300 -
all-1445 -
obs--94 %
Refinement TLS params.Method: refined / Origin x: -2.6945 Å / Origin y: -1.2041 Å / Origin z: 6.5345 Å
111213212223313233
T0.0432 Å2-0.0009 Å2-0.0058 Å2-0.0386 Å2-0.001 Å2--0.037 Å2
L1.3674 °20.1206 °20.4301 °2-0.2267 °20.088 °2--0.1474 °2
S-0.0345 Å °-0.0637 Å °-0.013 Å °-0.0156 Å °-0.0109 Å °-0.0264 Å °0.0245 Å °-0.0569 Å °0.0244 Å °
Refinement TLS groupSelection details: all

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