Vacuolar protein sorting-associated protein 4B (VPS4B) is a 444-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O75351.
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The mean pLDDT of this model is 85.9 (confident overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 65% |
| 70 to 90 | Confident: backbone generally right | 21% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 7% |
What pLDDT means and how to read it
Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their ATP-dependent disassembly, possibly in combination with membrane fission (PubMed:18687924). Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. VPS4A/B are required for the exosomal release of SDCBP, CD63 and syndecan…
Proposed to be monomeric or homodimeric in nucleotide-free form and to oligomerize upon binding to ATP to form two stacked hexameric or heptameric rings with a central pore through which ESCRT-III substrates are translocated in an ATP-dependent manner. In vitro, associates on the inside of a helical tubular structure formed by a CHMP2A-CHMP3 polymer. Interacts with CHMP1A, CHMP1B, CHMP2A, CHMP4B…
Late endosome membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4U7Y | X-ray | 2.5 Å | A=1-89 |
| 1XWI | X-ray | 2.8 Å | A=123-444 |
| 7L9X | X-ray | 2.81 Å | A=1-444 |
| 1WR0 | NMR | A=1-77 | |
| 2CPT | NMR | A=1-104 | |
| 2JQH | NMR | A=1-86 | |
| 2JQK | NMR | A=1-86 |
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