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- PDB-9kzb: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1 -

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Basic information

Entry
Database: PDB / ID: 9kzb
TitleCryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
ComponentsMajor ampullate spidroin 1
KeywordsPROTEIN FIBRIL / amyloid / silk
Biological speciesLatrodectus hesperus (western black widow)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsZhang, Y.L. / Dai, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
Authors: Zhang, Y.L. / Dai, B.
History
DepositionDec 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Major ampullate spidroin 1
F: Major ampullate spidroin 1
G: Major ampullate spidroin 1
H: Major ampullate spidroin 1
I: Major ampullate spidroin 1
A: Major ampullate spidroin 1
C: Major ampullate spidroin 1
D: Major ampullate spidroin 1
J: Major ampullate spidroin 1
E: Major ampullate spidroin 1
K: Major ampullate spidroin 1
L: Major ampullate spidroin 1


Theoretical massNumber of molelcules
Total (without water)580,86412
Polymers580,86412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Major ampullate spidroin 1


Mass: 48405.320 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: The protein that forms the fibril is a block protein composed of 16 repetitive motifs. Due to the inability to precisely identify which specific repetitive motif contributes to the core ...Details: The protein that forms the fibril is a block protein composed of 16 repetitive motifs. Due to the inability to precisely identify which specific repetitive motif contributes to the core sequence of the fibril, it is not possible to directly correlate the amino acid sequence of each chain with a particular repetitive motif of the protein. Based on the arrangement of these repetitive motifs, we ultimately constructed the atomic model.
Source: (gene. exp.) Latrodectus hesperus (western black widow)
Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Latrodectus hesperus (western black widow)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.15.2_3472 / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -177.57 ° / Axial rise/subunit: 2.35 Å / Axial symmetry: C1
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15847 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008918
ELECTRON MICROSCOPYf_angle_d0.7561212
ELECTRON MICROSCOPYf_dihedral_angle_d12.66456
ELECTRON MICROSCOPYf_chiral_restr0.056120
ELECTRON MICROSCOPYf_plane_restr0.003174

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