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- EMDB-8765: MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of T... -

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Basic information

Entry
Database: EMDB / ID: 8765
TitleMicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257
Map dataPeptide DLIIKGISVHI from the RRM2 of TDP-43, residues 247-257
SampleDLIIKGISVHI fibril:
TAR DNA-binding protein 43
Function / homologyEukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / RNA recognition motif domain / nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / negative regulation by host of viral transcription / distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific ...Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / RNA recognition motif domain / nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / negative regulation by host of viral transcription / distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific / 3'-UTR-mediated mRNA stabilization / response to endoplasmic reticulum stress / positive regulation of insulin secretion / mRNA 3'-UTR binding / RNA splicing / negative regulation of protein phosphorylation / mRNA processing / regulation of cell cycle / double-stranded DNA binding / transcription by RNA polymerase II / regulation of apoptotic process / negative regulation of gene expression / nuclear speck / DNA-binding transcription factor activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / TAR DNA-binding protein 43
Function and homology information
SourceHomo sapiens (human)
Methodelectron crystallography / cryo EM
AuthorsGuenther EL / Sawaya MR
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
Validation ReportPDB-ID: 5w52

SummaryFull reportAbout validation report
DateDeposition: Jun 13, 2017 / Header (metadata) release: Jul 19, 2017 / Map release: Feb 21, 2018 / Last update: Jun 6, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5w52
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8765.map.gz (map file in CCP4 format, 1681 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
52 pix
0.34 Å/pix.
= 34.138 Å
80 pix
0.44 Å/pix.
= 23.036 Å
101 pix
0.42 Å/pix.
= 33.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.443 Å / Y: 0.338 Å / Z: 0.417 Å
Density
Contour Level:0.14 (by author), 0.14 (movie #1):
Minimum - Maximum-0.22446074 - 0.7162638
Average (Standard dev.)0.0020431273 (0.11619716)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions8010152
Origin-59-84-19
Limit201632
Spacing5210180
CellA: 23.036 Å / B: 34.138 Å / C: 33.36 Å
α: 80.875 deg. / β: 86.373 deg. / γ: 89.775 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.4430.3380.417
M x/y/z5210180
origin x/y/z0.0000.0000.000
length x/y/z23.03634.13833.360
α/β/γ80.87586.37389.775
start NX/NY/NZ-59-19-84
NX/NY/NZ8052101
MAP C/R/S312
start NC/NR/NS-84-59-19
NC/NR/NS1018052
D min/max/mean-0.2240.7160.002

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Supplemental data

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Sample components

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Entire DLIIKGISVHI fibril

EntireName: DLIIKGISVHI fibril / Details: This peptide was synthesized and crystallized. / Number of components: 2

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Component #1: protein, DLIIKGISVHI fibril

ProteinName: DLIIKGISVHI fibril / Details: This peptide was synthesized and crystallized. / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, TAR DNA-binding protein 43

ProteinName: TAR DNA-binding protein 43 / Recombinant expression: No
MassTheoretical: 1.209479 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: 3D array / Method: cryo EM
Crystal parametersSpace group: P1 / A: 24.81 Å / B: 4.73 Å / C: 15.83 Å / Alpha: 80.88 deg. / Beta: 86.37 deg. / Gamma: 89.78 deg.
Sample solutionpH: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 3.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DIFFRACTION
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: electron crystallography
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding

Output model

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