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- EMDB-42398: MFAP4 after treatment with EDTA/without Ca2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-42398
TitleMFAP4 after treatment with EDTA/without Ca2+
Map dataD2 Relion4 reconstruction after postprocessing within Relion4 of MFAP4 after EDTA treatment.
Sample
  • Complex: MFAP4
    • Protein or peptide: MFAP4
KeywordsMFAP4 Octamer Extracellular Matrix / CELL ADHESION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsWozny MR / Nelea V / Siddiqui IFS / Wanga S / de Waard V / Strauss M / Reinhardt DP
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2024
Title: Microfibril-associated glycoprotein 4 forms octamers that mediate interactions with elastogenic proteins and cells.
Authors: Michael R Wozny / Valentin Nelea / Iram Fatima S Siddiqui / Shaynah Wanga / Vivian de Waard / Mike Strauss / Dieter P Reinhardt /
Abstract: Microfibril-associated glycoprotein 4 (MFAP4) is a 36-kDa extracellular matrix glycoprotein with critical roles in organ fibrosis, chronic obstructive pulmonary disease, and cardiovascular ...Microfibril-associated glycoprotein 4 (MFAP4) is a 36-kDa extracellular matrix glycoprotein with critical roles in organ fibrosis, chronic obstructive pulmonary disease, and cardiovascular disorders, including aortic aneurysms. MFAP4 multimerises and interacts with elastogenic proteins, including fibrillin-1 and tropoelastin, and with cells via integrins. Structural details of MFAP4 and its potential interfaces for these interactions are unknown. Here, we present a cryo-electron microscopy structure of human MFAP4. In the presence of calcium, MFAP4 assembles as an octamer, where two sets of homodimers constitute the top and bottom halves of each octamer. Each homodimer is linked together by an intermolecular disulphide bond. A C34S missense mutation prevents disulphide-bond formation between monomers but does not prevent octamer assembly. The atomic model, built into the 3.55 Å cryo-EM map, suggests that salt-bridge interactions mediate homodimer assembly, while non-polar residues form the interface between octamer halves. In the absence of calcium, an MFAP4 octamer dissociates into two tetramers. Binding studies with fibrillin-1, tropoelastin, LTBP4, and small fibulins show that MFAP4 has multiple surfaces for protein-protein interactions, most of which depend upon MFAP4 octamer assembly. The C34S mutation does not affect these protein interactions or cell interactions. MFAP4 assemblies with fibrillin-1 abrogate MFAP4 interactions with cells.
History
DepositionOct 18, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42398.png

Downloads & links

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Map

FileDownload / File: emd_42398.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD2 Relion4 reconstruction after postprocessing within Relion4 of MFAP4 after EDTA treatment.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 160 pix.
= 187.36 Å		1.17 Å/pix.
x 160 pix.
= 187.36 Å		1.17 Å/pix.
x 160 pix.
= 187.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0248
Minimum - Maximum-0.05123566 - 0.15518774
Average (Standard dev.)-0.000050591992 (±0.004507692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 187.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map from D2 Relion4 refinement of MFAP4 after EDTA treatment.

Fileemd_42398_half_map_1.map
AnnotationHalf map from D2 Relion4 refinement of MFAP4 after EDTA treatment.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map from D2 Relion4 refinement of MFAP4 after EDTA treatment.

Fileemd_42398_half_map_2.map
AnnotationHalf map from D2 Relion4 refinement of MFAP4 after EDTA treatment.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MFAP4

EntireName: MFAP4
Components
  • Complex: MFAP4
    • Protein or peptide: MFAP4

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Supramolecule #1: MFAP4

SupramoleculeName: MFAP4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: MFAP4 treated with EDTA and dialysed against TBS without Ca2+
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: MFAP4

MacromoleculeName: MFAP4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CLQQPLDCDD IYAQGYQSDG VYLIYPSGPS VPVPVFCDMT TEGGKWTVFQ KRFNGSVSFF RGWNDYKLGF GRADGEYWLG LQNMHLLTLK QKYELRVDLE DFENNTAYAK YADFSISPNA VSAEEDGYTL FVAGFEDGGA GDSLSYHSGQ KFSTFDRDQD LFVQNCAALS ...String:
CLQQPLDCDD IYAQGYQSDG VYLIYPSGPS VPVPVFCDMT TEGGKWTVFQ KRFNGSVSFF RGWNDYKLGF GRADGEYWLG LQNMHLLTLK QKYELRVDLE DFENNTAYAK YADFSISPNA VSAEEDGYTL FVAGFEDGGA GDSLSYHSGQ KFSTFDRDQD LFVQNCAALS SGAFWFRSCH FANLNGFYLG GSHLSYANGI NWAQWKGFYY SLKRTEMKIR RA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 578476
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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