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- PDB-5w7v: CryoEM structure of the segment, DLIIKGISVHI, assembled into a tr... -

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Basic information

Entry
Database: PDB / ID: 5w7v
TitleCryoEM structure of the segment, DLIIKGISVHI, assembled into a triple-helical fibril
ComponentsTAR DNA-binding protein 43
KeywordsPROTEIN FIBRIL / Amyloid / steric zipper
Function/homologynuclear inner membrane organization / negative regulation by host of viral transcription / 3'-UTR-mediated mRNA stabilization / mRNA 3'-UTR binding / RNA splicing / negative regulation of protein phosphorylation / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / mRNA processing / RNA-binding domain superfamily ...nuclear inner membrane organization / negative regulation by host of viral transcription / 3'-UTR-mediated mRNA stabilization / mRNA 3'-UTR binding / RNA splicing / negative regulation of protein phosphorylation / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / mRNA processing / RNA-binding domain superfamily / regulation of cell cycle / double-stranded DNA binding / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / transcription by RNA polymerase II / Nucleotide-binding alpha-beta plait domain superfamily / regulation of apoptotic process / negative regulation of gene expression / DNA binding transcription factor activity / RNA binding / nucleoplasm / identical protein binding / nucleus / TAR DNA-binding protein 43
Function and homology information
Specimen sourceHomo sapiens / human /
MethodElectron microscopy (3.8 Å resolution / Helical array / Helical) / Transmission electron microscopy
AuthorsGuenther, E.L. / Ge, P. / Eisenberg, D.S.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2017 / Release: Mar 14, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 14, 2018Structure modelrepositoryInitial release
1.1Mar 28, 2018Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Apr 18, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8781
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Assembly

Deposited unit
1: TAR DNA-binding protein 43
3: TAR DNA-binding protein 43
2: TAR DNA-binding protein 43
6: TAR DNA-binding protein 43
5: TAR DNA-binding protein 43
4: TAR DNA-binding protein 43
7: TAR DNA-binding protein 43
0: TAR DNA-binding protein 43
8: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)10,8859
Polyers10,8859
Non-polymers00
Water0
1
1: TAR DNA-binding protein 43
3: TAR DNA-binding protein 43
2: TAR DNA-binding protein 43
6: TAR DNA-binding protein 43
5: TAR DNA-binding protein 43
4: TAR DNA-binding protein 43
7: TAR DNA-binding protein 43
0: TAR DNA-binding protein 43
8: TAR DNA-binding protein 43
x 30


Theoretical massNumber of molelcules
Total (without water)326,559270
Polyers326,559270
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation30
2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 30 / Rise per n subunits: 1.598 Å / Rotation per n subunits: -120.441 deg.

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Components

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


Mass: 1209.479 Da / Num. of mol.: 9 / Fragment: RRM2 peptide (UNP residues 247-257) / Source: (synth.) Homo sapiens / human / / References: UniProt:Q13148

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

ComponentName: DLIIKGISVHI fibril / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 7
Buffer componentName: Water / Formula: H2O
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 610
EM imaging opticsEnergyfilter name: Gatan Quantum
Image scansMovie frames/image: 50 / Used frames/image: 4-20

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN1.9PARTICLE SELECTION
2Leginon3.2IMAGE ACQUISITION
4CTFFIND4.0CTF CORRECTION
12RELION1.4RECONSTRUCTION+IHRSR implementation
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -120.441 deg. / Axial rise/subunit: 1.598 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 18818 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00720370
ELECTRON MICROSCOPYf_angle_d0.77127210
ELECTRON MICROSCOPYf_dihedral_angle_d10.10612300
ELECTRON MICROSCOPYf_chiral_restr0.0633840
ELECTRON MICROSCOPYf_plane_restr0.0023060

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