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- PDB-5w52: MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of T... -

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Basic information

Entry
Database: PDB / ID: 5w52
TitleMicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257
ComponentsTAR DNA-binding protein 43
KeywordsPROTEIN FIBRIL / Amyloid / steric zipper
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 non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / molecular condensate scaffold activity / response to endoplasmic reticulum stress ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / molecular condensate scaffold activity / response to endoplasmic reticulum stress / RNA splicing / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / positive regulation of insulin secretion / mRNA processing / cytoplasmic stress granule / positive regulation of protein import into nucleus / rhythmic process / double-stranded DNA binding / regulation of gene expression / 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 / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-terminal domain / 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)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / molecular replacement / cryo EM / Resolution: 1.4 Å
AuthorsGuenther, E.L. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1616265 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.
Authors: Elizabeth L Guenther / Peng Ge / Hamilton Trinh / Michael R Sawaya / Duilio Cascio / David R Boyer / Tamir Gonen / Z Hong Zhou / David S Eisenberg /
Abstract: Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a ...Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the DLIIKGISVHI segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.
History
DepositionJun 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
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 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Jun 30, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.8Mar 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 1.9Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)1,2091
Polymers1,2091
Non-polymers00
Water0
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)12,09510
Polymers12,09510
Non-polymers00
Water0
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 operation1_554x,y,z-11
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_574x,y+2,z-11
crystal symmetry operation1_544x,y-1,z-11
crystal symmetry operation1_534x,y-2,z-11
Unit cell
Length a, b, c (Å)24.810, 4.730, 15.830
Angle α, β, γ (deg.)80.880, 86.370, 89.780
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 1209.479 Da / Num. of mol.: 1 / Fragment: RRM2 peptide (UNP residues 247-257) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13148

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: DLIIKGISVHI fibril / Type: COMPLEX / Details: This peptide was synthesized and crystallized. / Entity ID: all / Source: NATURAL
Molecular weightValue: 5.03 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE
CrystalDensity Matthews: 1.51 Å3/Da / Density % sol: 18.73 %
Crystal growTemperature: 310 K / Method: batch / pH: 8.5 / Details: 50 mM CHES, pH 8.5

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Data collection

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 3.4 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM diffractionCamera length: 1840 mm
EM diffraction shellResolution: 1.4→1.48 Å / Fourier space coverage: 62.1 % / Multiplicity: 6.71 / Num. of structure factors: 139 / Phase residual: 0.001 °
EM diffraction statsFourier space coverage: 73.4 % / High resolution: 1.4 Å / Num. of intensities measured: 9353 / Num. of structure factors: 1037 / Phase error: 0.001 ° / Phase residual: 0.001 ° / Phase error rejection criteria: 1 / Rmerge: 20.3 / Rsym: 20.3
DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251 Å
DetectorType: TVIPS F416 CMOS CAMERA / Detector: CMOS / Date: Jan 19, 2017
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11-H, K, K-L20.501
ReflectionResolution: 1.4→15.6 Å / Num. obs: 1037 / % possible obs: 73.4 % / Observed criterion σ(I): -3 / Redundancy: 9.019 % / Biso Wilson estimate: 21.481 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.203 / Rrim(I) all: 0.213 / Χ2: 0.595 / Net I/σ(I): 3.34 / Num. measured all: 9353 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.486.7121.4510.929332241390.3331.56262.1
1.48-1.5710.0390.7562.1118072201800.8170.79481.8
1.57-1.677.5180.3732.268271561100.9890.39670.5
1.67-1.818.4791.0121.9710091561190.7091.07776.3
1.81-1.989.4050.4853.4110911541160.9460.5175.3
1.98-2.2110.7070.3814.8212421571160.9070.40373.9
2.21-2.5610.4430.2415.08919121880.9270.25672.7
2.56-3.137.7680.2874.9753695690.9510.30472.6
3.13-4.439.8970.1917.1877293780.9870.283.9
4.43-15.69.8640.1387.4521737220.9980.14259.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
EM software
IDNameVersionCategory
1TVIPSF416image acquisition
6Cootmodel fitting
8Phasermolecular replacement
11XSCALEcrystallography merging
13REFMACmodel refinement
EM 3D crystal entity∠α: 80.88 ° / ∠β: 86.37 ° / ∠γ: 89.78 ° / A: 24.81 Å / B: 4.73 Å / C: 15.83 Å / Space group name: P1 / Space group num: 1
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealized 11-residue beta strand

Resolution: 1.4→15.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.788 / SU ML: 0.104 / SU R Cruickshank DPI: 0.0326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3065 92 8.9 %RANDOM
Rwork0.2619 ---
obs0.2655 944 72.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.54 Å2 / Biso mean: 33.756 Å2 / Biso min: 15.63 Å2
Baniso -1Baniso -2Baniso -3
1-20.78 Å2-1.04 Å2-18.05 Å2
2---25.77 Å2-3.48 Å2
3---4.98 Å2
Refinement stepCycle: final / Resolution: 1.39→15.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms84 0 0 0 84
Num. residues----11
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0090.01984
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0170.0298
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.2111.979112
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.7763225
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg6.438510
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg23.273252
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg7.471518
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0790.216
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0040.0280
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other00.0214
LS refinement shellResolution: 1.392→1.428 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 3 -
Rwork0.409 43 -
all-46 -
obs--36.22 %

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