Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation. Determined by electron microscopy at 3.9 Å resolution. Released 20 Aug 2025.
Explore 9AZ3 in 3D Show helices and sheets RCSB PDB PDBe
9AZ3 contains 13 α-helices and 37 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 55-56 | 2 | 1 |
| β-strand | 63-64 | 2 | 2 |
| β-strand | 76-77 | 2 | 3 |
| β-strand | 89-90 | 2 | 3 |
| α-helix | 103-106 | 4 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 123-125 | 3 | |
| β-strand | 134-137 | 4 | 2 |
| β-strand | 143 | 1 | 4 |
| β-strand | 144 | 1 | 5 |
| β-strand | 147-152 | 6 | 1 |
| β-strand | 159-165 | 7 | 2 |
| β-strand | 172-179 | 8 | 2 |
| α-helix | 182-185 | 4 | |
| β-strand | 206 | 1 | 2 |
| β-strand | 218 | 1 | 1 |
| β-strand | 221-223 | 3 | 1 |
| α-helix | 234-236 | 3 | |
| α-helix | 238-244 | 7 | |
| β-strand | 245 | 1 | 5 |
| β-strand | 248-252 | 5 | 2 |
| α-helix | 267-272 | 6 | |
| β-strand | 276-284 | 9 | 1 |
| β-strand | 286 | 1 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 49 | 1 | 6 |
| β-strand | 61 | 1 | 7 |
| β-strand | 66 | 1 | 8 |
| β-strand | 72 | 1 | 8 |
| β-strand | 78 | 1 | 7 |
| β-strand | 81 | 1 | 9 |
| β-strand | 88 | 1 | 9 |
| α-helix | 91-93 | 3 | |
| α-helix | 103-105 | 3 | |
| β-strand | 117 | 1 | 6 |
| β-strand | 125-126 | 2 | 10 |
| β-strand | 130 | 1 | 11 |
| α-helix | 137-139 | 3 | |
| β-strand | 142-146 | 5 | 12 |
| β-strand | 158 | 1 | 12 |
| α-helix | 164-167 | 4 | |
| β-strand | 198 | 1 | 11 |
| α-helix | 203-205 | 3 | |
| α-helix | 213-216 | 4 | |
| α-helix | 217-219 | 3 | |
| β-strand | 220-221 | 2 | 10 |
| β-strand | 224-228 | 5 | 12 |
| β-strand | 271 | 1 | 13 |
| β-strand | 293 | 1 | 13 |
| β-strand | 299-300 | 2 | 14 |
| β-strand | 306-307 | 2 | 14 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Laminin subunit gamma-1 | G | protein | 305 | Homo sapiens | P11047 (AlphaFold model) |
| Netrin-4 | N | protein | 284 | Mus musculus | Q9JI33 (AlphaFold model) |
>9AZ3_1 Laminin subunit gamma-1 (chains G) MDECTDEGGRPQRCMPEFVNAAFNVTVVATNTCGTPPEEYCVQTGVTGVTKSCHLCDAGQ PHLQHGAAFLTDYNNQADTTWWQSQTMLAGVQYPSSINLTLHLGKAFDITYVRLKFHTSR PESFAIYKRTWEDGPWIPYQYYSGSCENTYSKANRGFIRTGGDEQQALCTDEFSDISPLT GGNVAFSTLEGRPSAYNFDNSPVLQEWVTATDISVTLNRLNTFGDEVFNRPKVLKSYYYA ISDFAVGGRCKCNGHASECMKNEFDKLVCNCKHNTYGVDCEKCLPFFNDRPWRRATAESA SECLP
>9AZ3_2 Netrin-4 (chains N) LGRKLRADTMCGQNATELFCFYSENADLTCRQPKCDKCNAAHSHLAHPPSAMADSSFRFP RTWWQSAEDVHREKIQLDLEAEFYFTHLIMVFKSPRPAAMVLDRSQDFGKTWKPYKYFAT NCSATFGLEDDVVKKGAICTSRYSNPFPCTGGEVIFRALSPPYDIENPYSAKVQEQLKIT NLRVRLLKRQSCPCQINDLNAKPHHFMHYAVYDFIVKGSCFCNGHADQCLPVEGFRPIKA PGAFHVVHGRCMCKHNTAGSHCQHCAPLYNDRPWEAADGRTGAP
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 7 |
Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation. Kulczyk, A.W., McKee, K.K., Yurchenco, P.D. Nat Commun (2025) 16:7256-7256. DOI 10.1038/s41467-025-62814-7 · PubMed
Other PDB entries of the same protein (UniProt P11047 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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