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- EMDB-13986: Fibrillin-1 microfibril arm-region -

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Basic information

Entry
Database: EMDB / ID: EMD-13986
TitleFibrillin-1 microfibril arm-region
Map dataFibrillin microfibril arm-region
Sample
  • Tissue: Fibrillin-1 microfibril arm region
KeywordsMicrofibril / Extra-Cellular-Matrix / STRUCTURAL PROTEIN
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.3 Å
AuthorsGodwin ARF / Thomson J / Holmes DF / Adamo CS / Sengle G / Sherratt MJ / Roseman AM / Baldock C
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N015398/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S015779/1 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Fibrillin microfibril structure identifies long-range effects of inherited pathogenic mutations affecting a key regulatory latent TGFβ-binding site.
Authors: Alan R F Godwin / Rana Dajani / Xinyang Zhang / Jennifer Thomson / David F Holmes / Christin S Adamo / Gerhard Sengle / Michael J Sherratt / Alan M Roseman / Clair Baldock /
Abstract: Genetic mutations in fibrillin microfibrils cause serious inherited diseases, such as Marfan syndrome and Weill-Marchesani syndrome (WMS). These diseases typically show major dysregulation of tissue ...Genetic mutations in fibrillin microfibrils cause serious inherited diseases, such as Marfan syndrome and Weill-Marchesani syndrome (WMS). These diseases typically show major dysregulation of tissue development and growth, particularly in skeletal long bones, but links between the mutations and the diseases are unknown. Here we describe a detailed structural analysis of native fibrillin microfibrils from mammalian tissue by cryogenic electron microscopy. The major bead region showed pseudo eightfold symmetry where the amino and carboxy termini reside. On the basis of this structure, we show that a WMS deletion mutation leads to the induction of a structural rearrangement that blocks interaction with latent TGFβ-binding protein-1 at a remote site. Separate deletion of this binding site resulted in the assembly of shorter fibrillin microfibrils with structural alterations. The integrin αβ-binding site was also mapped onto the microfibril structure. These results establish that in complex extracellular assemblies, such as fibrillin microfibrils, mutations may have long-range structural consequences leading to the disruption of growth factor signaling and the development of disease.
History
DepositionDec 14, 2021-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13986.png

Downloads & links

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Map

FileDownload / File: emd_13986.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFibrillin microfibril arm-region
Voxel sizeX=Y=Z: 2.22 Å
Density
Contour LevelBy AUTHOR: 0.031
Minimum - Maximum-0.0048498637 - 0.07719506
Average (Standard dev.)0.0008700693 (±0.005258685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Fibrillin microfibril arm-region with bread region density removed

Fileemd_13986_additional_1.map
AnnotationFibrillin microfibril arm-region with bread region density removed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fibrillin-1 microfibril arm region

EntireName: Fibrillin-1 microfibril arm region
Components
  • Tissue: Fibrillin-1 microfibril arm region

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Supramolecule #1: Fibrillin-1 microfibril arm region

SupramoleculeName: Fibrillin-1 microfibril arm region / type: tissue / ID: 1 / Parent: 0
Details: Microfibrils generated from sonication of bovine ciliary zonule tissue.
Source (natural)Organism: Bos taurus (cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTis-HClTris base
2.0 mMCaCl2Calcium Chloride

Details: Solutions were made fresh and filtered using 0.2 um filters.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Frames/image: 1-20 / Number grids imaged: 1 / Average exposure time: 20.0 sec. / Average electron dose: 66.0 e/Å2 / Details: Movies were collected in counting mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 27737
Startup modelType of model: OTHER
Details: A negative stain reconstruction of a microfibril was used as an initial model.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4957
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Details: Model was refined using cryosparc using homogeneous refine
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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