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- EMDB-21816: Cryo-EM of Form 2 like peptide filament, 29-20-2 -

Open data

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Basic information

Database: EMDB / ID: EMD-21816
TitleCryo-EM of Form 2 like peptide filament, 29-20-2
Map data
Sampleself-assembly peptide filament, 29-20-2:
peptide 29-20-2
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang F / Gnewou OM / Modlin C / 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 2 like peptide filament, 29-20-2
Authors: Wang F / Gnewou OM / Modlin C / Egelman EH / Conticello VP
Validation ReportPDB-ID: 6wl7

SummaryFull reportAbout validation report
DepositionApr 18, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0111
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0111
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wl7
  • Surface level: 0.0111
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wl7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_21816.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Contour LevelBy AUTHOR: 0.0111 / Movie #1: 0.0111
Minimum - Maximum-0.010292183 - 0.026565412
Average (Standard dev.)0.0003704461 (±0.0018988289)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
start NX/NY/NZ79740
MAP C/R/S123
start NC/NR/NS-160-160-160
D min/max/mean-0.0100.0270.000

Supplemental data

Sample components

Entire self-assembly peptide filament, 29-20-2

EntireName: self-assembly peptide filament, 29-20-2 / Details: synthetic peptide / Number of components: 2

Component #1: protein, self-assembly peptide filament, 29-20-2

ProteinName: self-assembly peptide filament, 29-20-2 / Details: synthetic peptidePeptide synthesis / Recombinant expression: No
SourceSpecies: synthetic construct (others)

Component #2: protein, peptide 29-20-2

ProteinName: peptide 29-20-2 / Number of Copies: 150 / Recombinant expression: No
MassTheoretical: 3.253769 kDa
SourceSpecies: synthetic construct (others)

Experimental details

Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C3 (3 fold cyclic) / Delta z: 5.63 Å / Delta phi: 12.9 %deg;
Sample solutionpH: 7
Support filmunspecified
VitrificationCryogen name: ETHANE

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: 55 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 3.8 Å / Resolution method: OTHER / Details: Model:Map FSC 0.38 cut off and d99

Atomic model buiding

Output model

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