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- PDB-9oek: amyloid fibril of recombinant transforming growth factor beta ind... -

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Basic information

Entry
Database: PDB / ID: 9oek
Titleamyloid fibril of recombinant transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
ComponentsTransforming growth factor-beta-induced protein ig-h3
KeywordsPROTEIN FIBRIL / amyloid fibril / corneal dystrophy
Function / homology
Function and homology information


elastic fiber / microfibril / negative regulation of cell adhesion / chondrocyte differentiation / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / collagen binding / visual perception ...elastic fiber / microfibril / negative regulation of cell adhesion / chondrocyte differentiation / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / collagen binding / visual perception / cell adhesion molecule binding / trans-Golgi network / integrin binding / cell population proliferation / angiogenesis / extracellular matrix / cell adhesion / Amyloid fiber formation / : / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / : / Fasciclin domain / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile.
Similarity search - Domain/homology
Transforming growth factor-beta-induced protein ig-h3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsJiang, Y.X. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG070895 United States
CitationJournal: To Be Published
Title: Structure of TGFBIp amyloid fibril driven by a corneal dystrophy-causing mutation
Authors: Jiang, Y.X. / Sawaya, M.R. / Salwinski, L. / Ge, P. / Wang, C. / Hu, C.J. / Hernandez, H. / Boyer, D.R. / Melo, F. / Eisenberg, D.S.
History
DepositionApr 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / 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: Transforming growth factor-beta-induced protein ig-h3
B: Transforming growth factor-beta-induced protein ig-h3
C: Transforming growth factor-beta-induced protein ig-h3
D: Transforming growth factor-beta-induced protein ig-h3
E: Transforming growth factor-beta-induced protein ig-h3
F: Transforming growth factor-beta-induced protein ig-h3
G: Transforming growth factor-beta-induced protein ig-h3
H: Transforming growth factor-beta-induced protein ig-h3
I: Transforming growth factor-beta-induced protein ig-h3
J: Transforming growth factor-beta-induced protein ig-h3


Theoretical massNumber of molelcules
Total (without water)168,96310
Polymers168,96310
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
Transforming growth factor-beta-induced protein ig-h3 / Beta ig-h3 / Kerato-epithelin / RGD-containing collagen-associated protein / RGD-CAP


Mass: 16896.295 Da / Num. of mol.: 10 / Fragment: FAS1-4 domain / Mutation: V624M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBI, BIGH3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15582
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: transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.21 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C2
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2263 / Symmetry type: HELICAL
Atomic model buildingB value: 93.8 / Space: REAL
RefinementHighest resolution: 3.24 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033080
ELECTRON MICROSCOPYf_angle_d0.6374130
ELECTRON MICROSCOPYf_dihedral_angle_d13.0081150
ELECTRON MICROSCOPYf_chiral_restr0.047520
ELECTRON MICROSCOPYf_plane_restr0.004510

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