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- PDB-9nfn: Nanotube of Y5 - (5 protomer) -

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Basic information

Entry
Database: PDB / ID: 9nfn
TitleNanotube of Y5 - (5 protomer)
ComponentsY5
KeywordsPROTEIN FIBRIL / Peptide nanotube / Amphiphile / Amyloids / helical
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsDas, A. / Conticello, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Nanotube of Y5 - (5 promoter)
Authors: Das, A. / Conticello, V.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Y5
1: Y5
2: Y5
3: Y5
4: Y5
5: Y5
6: Y5
7: Y5
8: Y5
9: Y5
AA: Y5
AB: Y5
AC: Y5
AD: Y5
AE: Y5
AF: Y5
AG: Y5
AH: Y5
AI: Y5
AJ: Y5
AK: Y5
AL: Y5
AM: Y5
AN: Y5
AO: Y5
AP: Y5
AQ: Y5
AR: Y5
AS: Y5
AT: Y5
AU: Y5
AV: Y5
AW: Y5
AX: Y5
AY: Y5
AZ: Y5
Aa: Y5
Ab: Y5
Ac: Y5
Ad: Y5
Ae: Y5
Af: Y5
Ag: Y5
Ah: Y5
Ai: Y5
Aj: Y5
Ak: Y5
Al: Y5
Am: Y5
An: Y5
Ao: Y5
Ap: Y5
Aq: Y5
Ar: Y5
As: Y5
At: Y5
Au: Y5
Av: Y5
Aw: Y5
f: Y5
g: Y5
h: Y5
i: Y5
j: Y5
k: Y5
l: Y5
m: Y5
n: Y5
o: Y5
p: Y5
q: Y5
r: Y5
s: Y5
t: Y5
u: Y5
v: Y5
w: Y5
x: Y5
y: Y5
z: Y5


Theoretical massNumber of molelcules
Total (without water)64,24580
Polymers64,24580
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Y5


Mass: 803.068 Da / Num. of mol.: 80 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Synthetic nanotube / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.039 ° / Axial rise/subunit: 4.924 Å / Axial symmetry: C5
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64499 / Symmetry type: HELICAL
Atomic model buildingB value: 20.4

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