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- EMDB-42394: Single particle analysis of recombinant human MFAP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-42394
TitleSingle particle analysis of recombinant human MFAP4
Map dataD2 map after Relion4 postprocess and z-axis flip
Sample
  • Complex: Octamer assembly of MFAP4
    • Protein or peptide: Microfibril-associated glycoprotein 4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsMFAP4 Octamer Extracellular Matrix / CELL ADHESION
Function / homology
Function and homology information


regulation of collagen metabolic process / elastic fiber / microfibril / elastic fiber assembly / UV protection / Molecules associated with elastic fibres / cellular response to UV-B / supramolecular fiber organization / collagen-containing extracellular matrix / cell adhesion ...regulation of collagen metabolic process / elastic fiber / microfibril / elastic fiber assembly / UV protection / Molecules associated with elastic fibres / cellular response to UV-B / supramolecular fiber organization / collagen-containing extracellular matrix / cell adhesion / extracellular space / extracellular region
Similarity search - Function
Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Microfibril-associated glycoprotein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsWozny MW / Nelea V
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_42394.png

Downloads & links

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Map

FileDownload / File: emd_42394.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD2 map after Relion4 postprocess and z-axis flip
Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.00908
Minimum - Maximum-0.03288211 - 0.0548213
Average (Standard dev.)0.0000734777 (±0.0016746221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: D2 half map after Relion4 refine3d

Fileemd_42394_half_map_1.map
AnnotationD2 half map after Relion4 refine3d
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: D2 half map after Relion4 refine3d

Fileemd_42394_half_map_2.map
AnnotationD2 half map after Relion4 refine3d
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octamer assembly of MFAP4

EntireName: Octamer assembly of MFAP4
Components
  • Complex: Octamer assembly of MFAP4
    • Protein or peptide: Microfibril-associated glycoprotein 4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Octamer assembly of MFAP4

SupramoleculeName: Octamer assembly of MFAP4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 kDa/nm

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Macromolecule #1: Microfibril-associated glycoprotein 4

MacromoleculeName: Microfibril-associated glycoprotein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.440645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVSGIRGDAL ERFCLQQPLD CDDIYAQGYQ SDGVYLIYPS GPSVPVPVFC DMTTEGGKWT VFQKRFNGSV SFFRGWNDYK LGFGRADGE YWLGLQNMHL LTLKQKYELR VDLEDFENNT AYAKYADFSI SPNAVSAEED GYTLFVAGFE DGGAGDSLSY H SGQKFSTF ...String:
QVSGIRGDAL ERFCLQQPLD CDDIYAQGYQ SDGVYLIYPS GPSVPVPVFC DMTTEGGKWT VFQKRFNGSV SFFRGWNDYK LGFGRADGE YWLGLQNMHL LTLKQKYELR VDLEDFENNT AYAKYADFSI SPNAVSAEED GYTLFVAGFE DGGAGDSLSY H SGQKFSTF DRDQDLFVQN CAALSSGAFW FRSCHFANLN GFYLGGSHLS YANGINWAQW KGFYYSLKRT EMKIRRAGKP IP NPLLGLD STRTGHHHHH HHH

UniProtKB: Microfibril-associated glycoprotein 4

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
GridModel: C-flat / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 455190
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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