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- PDB-5wkd: Crystal structure of the segment, GNNQGSN, from the low complexit... -

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Basic information

Entry
Database: PDB / ID: 5wkd
TitleCrystal structure of the segment, GNNQGSN, from the low complexity domain of TDP-43, residues 300-306
ComponentsTAR DNA-binding protein 43
KeywordsPROTEIN FIBRIL / TDP-43 / amyloid / low complexity domain
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 / regulation of circadian rhythm / positive regulation of insulin secretion / 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 / Resolution: 1.8 Å
AuthorsGuenther, E.L. / Trinh, H. / Sawaya, M.R. / Cascio, D. / 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 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 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
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 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
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)6901
Polymers6901
Non-polymers00
Water362
1
A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43

A: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)6,89610
Polymers6,89610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
crystal symmetry operation4_575-x+1/2,y+5/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_535-x+1/2,y-3/2,-z1
Unit cell
Length a, b, c (Å)50.347, 4.777, 14.746
Angle α, β, γ (deg.)90.000, 101.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

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


Mass: 689.634 Da / Num. of mol.: 1 / Fragment: UNP residues 300-306 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13148
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.26 Å3/Da / Density % sol: 2.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Bis-Tris propane, pH 7.5, 200 mM sodium sulfate, 20% PEG3350

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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: Aug 13, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 373 / % possible obs: 91.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.158 / Χ2: 2.003 / Net I/σ(I): 5.4 / Num. measured all: 845
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.862.20.25282.711184.8
1.86-1.942.40.254393.034188.6
1.94-2.032.20.316362.952192.3
2.03-2.132.40.164331.67197.1
2.13-2.272.30.285452.188190
2.27-2.4420.242352.095189.7
2.44-2.692.50.175351.611194.6
2.69-3.082.50.111361.492192.3
3.08-3.882.40.125410.818197.6
3.88-10020.075451.906190

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealized beta strand

Resolution: 1.8→24.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1803 / WRfactor Rwork: 0.1674 / FOM work R set: 0.8177 / SU B: 3.915 / SU ML: 0.114 / SU R Cruickshank DPI: 0.2052 / SU Rfree: 0.1412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 22 6 %RANDOM
Rwork0.1837 ---
obs0.1843 345 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 24.53 Å2 / Biso mean: 8.826 Å2 / Biso min: 4.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.14 Å2
2---0.24 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.8→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48 0 0 2 50
Biso mean---16.87 -
Num. residues----7
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01947
X-RAY DIFFRACTIONr_bond_other_d0.020.0230
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.87362
X-RAY DIFFRACTIONr_angle_other_deg0.838373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg61.302304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.174156
X-RAY DIFFRACTIONr_chiral_restr0.0970.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0262
X-RAY DIFFRACTIONr_gen_planes_other00.026
LS refinement shellResolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 1 -
Rwork0.293 23 -
all-24 -
obs--70.59 %

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