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- EMDB-21813: Cryo-EM of Form 1 related peptide filament, 29-24-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-21813
TitleCryo-EM of Form 1 related peptide filament, 29-24-3
Map data
Sampleself-assembly peptide filament, 29-24-3:
peptide 29-24-3
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang F / Gnewou OM / Egelman EH / Conticello VP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
CitationJournal: To Be Published
Title: Cryo-EM of Form 1 related peptide filament, 29-24-3
Authors: Wang F / Gnewou OM / Egelman EH / Conticello VP
Validation ReportPDB-ID: 6wky

SummaryFull reportAbout validation report
History
DepositionApr 17, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000713
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.000713
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wky
  • Surface level: 0.000713
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wky
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21813.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å
1.04 Å/pix.
x 320 pix.
= 332.8 Å
1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.000713 / Movie #1: 0.000713
Minimum - Maximum-0.00064017635 - 0.0017014847
Average (Standard dev.)0.0000007354 (±0.00010488522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire self-assembly peptide filament, 29-24-3

EntireName: self-assembly peptide filament, 29-24-3 / Details: synthetic peptide / Number of components: 2

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Component #1: protein, self-assembly peptide filament, 29-24-3

ProteinName: self-assembly peptide filament, 29-24-3 / Details: synthetic peptidePeptide synthesis / Recombinant expression: No
SourceSpecies: synthetic construct (others)

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Component #2: protein, peptide 29-24-3

ProteinName: peptide 29-24-3 / Number of Copies: 40 / Recombinant expression: No
MassTheoretical: 3.253769 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C4 (4 fold cyclic) / Delta z: 7.96 Å / Delta phi: 10.88 %deg;
Sample solutionpH: 7
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 54 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Details: Model:Map FSC 0.38 cut off and d99

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Atomic model buiding

Output model

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