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- PDB-9ku1: Cryo-electron microscopy structure of nanofibers formed by revers... -

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Basic information

Entry
Database: PDB / ID: 9ku1
TitleCryo-electron microscopy structure of nanofibers formed by reverse azobenzene peptides.
ComponentsAzoPep
KeywordsDE NOVO PROTEIN / nanofiber
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsKawabata, H. / Umezawa, H. / Park, S.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of AzoPep peptide nanofibers
Authors: Kawabata, H. / Umezawa, H. / Park, S.Y.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 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
A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep


Theoretical massNumber of molelcules
Total (without water)7,5907
Polymers7,5907
Non-polymers00
Water64936
1
A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep

A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep

A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep

A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep

A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep

A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep

A: AzoPep
B: AzoPep
C: AzoPep
D: AzoPep
E: AzoPep
F: AzoPep
G: AzoPep


Theoretical massNumber of molelcules
Total (without water)53,13149
Polymers53,13149
Non-polymers00
Water88349
TypeNameSymmetry operationNumber
point symmetry operation6
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
54generate(0.999549, -0.030015), (0.030015, 0.999549), (1)4.25253, -4.12674, -9.5064
55generate(-0.999747, 0.022513), (-0.022513, -0.999747), (1)275.99019, 282.27506, -7.1298
56generate(0.999887, -0.015009), (0.015009, 0.999887), (1)2.11078, -2.07933, -4.7532
57generate(-0.999972, 0.007505), (-0.007505, -0.999972), (1)278.11651, 280.21163, -2.3766
59generate(-0.999972, -0.007505), (0.007505, -0.999972), (1)280.21163, 278.11651, 2.3766
60generate(0.999887, 0.015009), (-0.015009, 0.999887), (1)-2.07933, 2.11078, 4.7532
62generate(0.999549, 0.030015), (-0.030015, 0.999549), (1)-4.12674, 4.25253, 9.5064

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Components

#1: Protein/peptide
AzoPep


Mass: 1084.302 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: AzoPep peptide nanofibers / Type: COMPLEX / Entity ID: #1 / Source: SYNTHETIC
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.57 ° / Axial rise/subunit: 2.3766 Å / Axial symmetry: C1
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92358 / Symmetry type: HELICAL

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