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- PDB-5wiq: Crystal structure of the segment, GFNGGFG, from the low complexit... -

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Basic information

Entry
Database: PDB / ID: 5wiq
TitleCrystal structure of the segment, GFNGGFG, from the low complexity domain of TDP-43, residues 396-402
ComponentsTAR 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 / 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: 1.25 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 19, 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 / 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 1.4Feb 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 1.6Oct 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

Downloads & links

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Assembly

Deposited unit
A: TAR DNA-binding protein 43
B: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)1,3092
Polymers1,3092
Non-polymers00
Water1448
1
A: TAR DNA-binding protein 43
B: TAR DNA-binding protein 43
x 5


Theoretical massNumber of molelcules
Total (without water)6,54710
Polymers6,54710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
Unit cell
Length a, b, c (Å)4.810, 16.439, 22.672
Angle α, β, γ (deg.)90.630, 96.370, 91.260
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 654.673 Da / Num. of mol.: 2 / Fragment: UNP residues 396-402 / Source method: obtained synthetically
Details: Synthetic peptide GFNGGFG corresponding tosegment 396-402 of TDP-43
Source: (synth.) Homo sapiens (human) / References: UniProt: Q13148
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.36 Å3/Da / Density % sol: 9.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM sodium acetate pH 4.5, 800mM sodium phosphate monobasic, 1200mM potassium phosphate dibasic

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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 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.25→100 Å / Num. obs: 1802 / % possible obs: 94.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 2.51 Å2 / Rmerge(I) obs: 0.161 / Χ2: 1.086 / Net I/σ(I): 5 / Num. measured all: 7394
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.25-1.291.80.4061661.389195.4
1.29-1.352.30.5021.082195.3
1.35-1.412.50.4371.077194
1.41-1.482.40.4210.927189.8
1.48-1.574.40.3241.099186
1.57-1.75.40.360.976193.9
1.7-1.875.40.2180.81100
1.87-2.145.50.1461.2271100
2.14-2.695.50.1171.093192.4
2.69-1005.50.0691.281199.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DENZOdata reduction
PDB_EXTRACT3.22data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WDB

5wdb
PDB Unreleased entry


Resolution: 1.25→22.53 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 14.98
RfactorNum. reflection% reflection
Rfree0.1678 180 10.02 %
Rwork0.1516 --
obs0.1533 1796 92.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 11.35 Å2 / Biso mean: 3.5085 Å2 / Biso min: 1.33 Å2
Refinement stepCycle: final / Resolution: 1.25→22.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94 0 0 8 102
Biso mean---7.65 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596
X-RAY DIFFRACTIONf_angle_d0.692124
X-RAY DIFFRACTIONf_chiral_restr0.1286
X-RAY DIFFRACTIONf_plane_restr0.00220
X-RAY DIFFRACTIONf_dihedral_angle_d7.49326
LS refinement shellResolution: 1.2424→22.5336 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1678 180 -
Rwork0.1516 1616 -
all-1796 -
obs--93 %
Refinement TLS params.Method: refined / Origin x: -0.2349 Å / Origin y: -1.8711 Å / Origin z: -12.5061 Å
111213212223313233
T0.0163 Å20.0038 Å2-0.004 Å2-0.0126 Å20.0042 Å2--0.0175 Å2
L0.5457 °20.0629 °20.1837 °2-0.8184 °20.3668 °2--0.7135 °2
S0.0173 Å °0.003 Å °-0.0104 Å °0.0076 Å °0.0093 Å °-0.0112 Å °0.0267 Å °0.0065 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 8
2X-RAY DIFFRACTION1allB1 - 7
3X-RAY DIFFRACTION1allC1 - 8

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