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- EMDB-34813: Structure of transforming growth factor beta induced protein (TGF... -

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Basic information

Entry
Database: EMDB / ID: EMD-34813
TitleStructure of transforming growth factor beta induced protein (TGFBIp) G623R fibril
Map data
Sample
  • Complex: Mutant of TGFBIp peptide derived from TGFBIp
    • Protein or peptide: Transforming growth factor-beta-induced protein ig-h3
KeywordsPathological fibrils / TGFBI related corneal dystrophy / PROTEIN FIBRIL
Function / homology
Function and homology information


negative regulation of cell adhesion / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / extracellular matrix organization / visual perception / extracellular matrix ...negative regulation of cell adhesion / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / extracellular matrix organization / visual perception / extracellular matrix / trans-Golgi network / integrin binding / angiogenesis / collagen-containing extracellular matrix / cell population proliferation / cell adhesion / Amyloid fiber formation / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / : / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Similarity search - Domain/homology
Transforming growth factor-beta-induced protein ig-h3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsLow JYK / Pervushin K
Funding support Singapore, 2 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2019-T3-1-012 Singapore
Ministry of Education (MoE, Singapore)RG28/19 Singapore
CitationJournal: Commun Biol / Year: 2023
Title: Release of frustration drives corneal amyloid disaggregation by brain chaperone.
Authors: Jia Yi Kimberly Low / Xiangyan Shi / Venkatraman Anandalakshmi / Dawn Neo / Gary Swee Lim Peh / Siew Kwan Koh / Lei Zhou / M K Abdul Rahim / Ketti Boo / JiaXuan Lee / Harini Mohanram / Reema ...Authors: Jia Yi Kimberly Low / Xiangyan Shi / Venkatraman Anandalakshmi / Dawn Neo / Gary Swee Lim Peh / Siew Kwan Koh / Lei Zhou / M K Abdul Rahim / Ketti Boo / JiaXuan Lee / Harini Mohanram / Reema Alag / Yuguang Mu / Jodhbir S Mehta / Konstantin Pervushin /
Abstract: TGFBI-related corneal dystrophy (CD) is characterized by the accumulation of insoluble protein deposits in the corneal tissues, eventually leading to progressive corneal opacity. Here we show that ...TGFBI-related corneal dystrophy (CD) is characterized by the accumulation of insoluble protein deposits in the corneal tissues, eventually leading to progressive corneal opacity. Here we show that ATP-independent amyloid-β chaperone L-PGDS can effectively disaggregate corneal amyloids in surgically excised human cornea of TGFBI-CD patients and release trapped amyloid hallmark proteins. Since the mechanism of amyloid disassembly by ATP-independent chaperones is unknown, we reconstructed atomic models of the amyloids self-assembled from TGFBIp-derived peptides and their complex with L-PGDS using cryo-EM and NMR. We show that L-PGDS specifically recognizes structurally frustrated regions in the amyloids and releases those frustrations. The released free energy increases the chaperone's binding affinity to amyloids, resulting in local restructuring and breakage of amyloids to protofibrils. Our mechanistic model provides insights into the alternative source of energy utilized by ATP-independent disaggregases and highlights the possibility of using these chaperones as treatment strategies for different types of amyloid-related diseases.
History
DepositionNov 19, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34813.png

Downloads & links

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Map

FileDownload / File: emd_34813.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00368
Minimum - Maximum-0.009534517 - 0.024628019
Average (Standard dev.)0.000046317506 (±0.0006309993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34813_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34813_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Mutant of TGFBIp peptide derived from TGFBIp

EntireName: Mutant of TGFBIp peptide derived from TGFBIp
Components
  • Complex: Mutant of TGFBIp peptide derived from TGFBIp
    • Protein or peptide: Transforming growth factor-beta-induced protein ig-h3

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Supramolecule #1: Mutant of TGFBIp peptide derived from TGFBIp

SupramoleculeName: Mutant of TGFBIp peptide derived from TGFBIp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.43 kDa/nm

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Macromolecule #1: Transforming growth factor-beta-induced protein ig-h3

MacromoleculeName: Transforming growth factor-beta-induced protein ig-h3 / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.547922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EPVAEPDIMA TNRVVHVITN VLQ

UniProtKB: Transforming growth factor-beta-induced protein ig-h3

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8 / Details: 20mM TRIS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -179.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48522
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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