+Open data
-Basic information
Entry | Database: PDB / ID: 8un7 | |||||||||
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Title | Single particle analysis of recombinant human MFAP4 | |||||||||
Components | Microfibril-associated glycoprotein 4 | |||||||||
Keywords | CELL ADHESION / MFAP4 Octamer Extracellular Matrix | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å | |||||||||
Authors | Wozny, M.W. / Nelea, V. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8un7.cif.gz | 354.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8un7.ent.gz | 289.4 KB | Display | PDB format |
PDBx/mmJSON format | 8un7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8un7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8un7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8un7_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 8un7_validation.cif.gz | 91.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/8un7 ftp://data.pdbj.org/pub/pdb/validation_reports/un/8un7 | HTTPS FTP |
-Related structure data
Related structure data | 42394MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 29440.645 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MFAP4 / Cell line (production host): HEK293-EBNA / Production host: Homo sapiens (human) / References: UniProt: P55083 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-CA / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Octamer assembly of MFAP4 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 280 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: HEK293-EBNA / Plasmid: pCEP4 |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 455190 / Symmetry type: POINT |