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- PDB-6cb9: Segment AALQSS from the low complexity domain of TDP-43, residues... -

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Basic information

Entry
Database: PDB / ID: 6cb9
TitleSegment AALQSS from the low complexity domain of TDP-43, residues 328-333
ComponentsAALQSS
KeywordsPROTEIN FIBRIL / Amyloid / Steric-zipper
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsGuenther, E.L. / Cao, Q. / Lu, J. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (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
DepositionFeb 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: AALQSS


Theoretical massNumber of molelcules
Total (without water)5761
Polymers5761
Non-polymers00
Water724
1
A: AALQSS
x 10


Theoretical massNumber of molelcules
Total (without water)5,75610
Polymers5,75610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
crystal symmetry operation4_766x+5/2,-y+3/2,-z+11
crystal symmetry operation4_666x+3/2,-y+3/2,-z+11
crystal symmetry operation4_366x-3/2,-y+3/2,-z+11
Unit cell
Length a, b, c (Å)4.790, 15.970, 42.430
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 AALQSS


Mass: 575.613 Da / Num. of mol.: 1 / Fragment: residues 328-333 / Source method: obtained synthetically
Details: Synthetic peptide AALQSS corresponding tosegment 328-333 of TDP-43
Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 1.41 Å3/Da / Density % sol: 12.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01 M Nickel Chloride hexahydrate, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→21.22 Å / Num. obs: 1432 / % possible obs: 90.7 % / Redundancy: 6.853 % / Biso Wilson estimate: 9.922 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.211 / Rrim(I) all: 0.23 / Χ2: 0.717 / Net I/σ(I): 5.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.147.2520.5622.821190.9130.60572.1
1.14-1.197.2820.5482.971310.8440.5978.4
1.19-1.247.3630.4373.721240.8640.4793.2
1.24-1.36.920.3194.151250.9730.343100
1.3-1.377.3580.3394.581370.9270.365100
1.37-1.466.8480.3464.461320.9080.37599.2
1.46-1.567.0650.2915.231080.960.31185
1.56-1.686.7580.2296.04990.9640.24986.1
1.68-1.847.0840.2376.33950.960.25496.9
1.84-2.066.980.1827.641010.9850.19599
2.06-2.386.5210.1957.27960.9840.2196
2.38-2.915.4240.1837.12590.9770.20390.8
2.91-4.125.9850.1547.6670.9660.17393.1
4.12-21.223.8210.1416.35390.9730.161100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
SHELXDphasing
RefinementResolution: 1.1→21.22 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.897 / SU B: 0.521 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.053
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 144 10.1 %RANDOM
Rwork0.195 ---
obs0.1994 1288 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 25.29 Å2 / Biso mean: 7.24 Å2 / Biso min: 3.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20 Å2
2--0.38 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.1→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40 0 0 4 44
Biso mean---19.98 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0239
X-RAY DIFFRACTIONr_bond_other_d0.0020.0237
X-RAY DIFFRACTIONr_angle_refined_deg1.4222.03152
X-RAY DIFFRACTIONr_angle_other_deg0.736386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.50555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg61.942301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.839156
X-RAY DIFFRACTIONr_chiral_restr0.10.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0243
X-RAY DIFFRACTIONr_gen_planes_other00.025
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 7 -
Rwork0.226 67 -
all-74 -
obs--67.27 %

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