8KA1: Rdtnd-rid cbd
Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin. Determined by X-ray diffraction at 2.82 Å resolution. Released 10 Jul 2024.
- Method
- X-ray diffraction
- Resolution
- 2.82 Å
- Organisms
- Vibrio vulnificus, Homo sapiens
- Chains
- 8
- Atoms
- 17,066
- Mol. weight
- 259.18 kDa
- Ligands
- MG
- Released
- 10 Jul 2024
Explore 8KA1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8KA1 contains 103 α-helices and 86 β-strands across 8 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.
Chain A: 20 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1983 | 15 | |
| α-helix | 1997-1998 | 2 | |
| α-helix | 2011-2025 | 15 | |
| α-helix | 2036-2048 | 13 | |
| α-helix | 2052-2063 | 12 | |
| β-strand | 2077-2079 | 3 | 1 |
| β-strand | 2080-2082 | 3 | 2 |
| α-helix | 2087-2095 | 9 | |
| β-strand | 2103-2105 | 3 | 1 |
| α-helix | 2107-2109 | 3 | |
| α-helix | 2111-2128 | 18 | |
| α-helix | 2136-2161 | 26 | |
| β-strand | 2166-2171 | 6 | 2 |
| β-strand | 2176-2177 | 2 | 3 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2195 | 9 | |
| β-strand | 2199-2205 | 7 | 2 |
| α-helix | 2209-2212 | 4 | |
| α-helix | 2217-2219 | 3 | |
| β-strand | 2222 | 1 | 2 |
| β-strand | 2231-2233 | 3 | 3 |
| α-helix | 2240-2246 | 7 | |
| α-helix | 2258-2259 | 2 | |
| β-strand | 2260-2261 | 2 | 3 |
| α-helix | 2266-2274 | 9 | |
| α-helix | 2280-2286 | 7 | |
| β-strand | 2288-2292 | 5 | 4 |
| β-strand | 2297-2301 | 5 | 4 |
| β-strand | 2310-2314 | 5 | 4 |
| α-helix | 2320-2333 | 14 | |
| α-helix | 2337-2339 | 3 | |
| β-strand | 2343-2347 | 5 | 4 |
| β-strand | 2350-2355 | 6 | 4 |
| β-strand | 2357-2363 | 7 | 4 |
| β-strand | 2369-2370 | 2 | 4 |
Chain B: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-18 | 12 | |
| β-strand | 21-22 | 2 | 5 |
| β-strand | 27-28 | 2 | 5 |
| α-helix | 30-40 | 11 | |
| α-helix | 46-55 | 10 | |
| α-helix | 66-79 | 14 | |
| α-helix | 82-91 | 10 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 103-113 | 11 | |
| α-helix | 119-129 | 11 | |
| β-strand | 136-138 | 3 | 6 |
| α-helix | 139-145 | 7 | |
Chain C: 15 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1985 | 17 | |
| α-helix | 1997-1998 | 2 | |
| α-helix | 2010-2025 | 16 | |
| α-helix | 2036-2049 | 14 | |
| α-helix | 2052-2063 | 12 | |
| β-strand | 2078-2079 | 2 | 7 |
| β-strand | 2081-2082 | 2 | 8 |
| α-helix | 2087-2097 | 11 | |
| β-strand | 2104-2105 | 2 | 7 |
| α-helix | 2111-2126 | 16 | |
| α-helix | 2139-2161 | 23 | |
| β-strand | 2166-2171 | 6 | 8 |
| β-strand | 2176-2177 | 2 | 9 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2194 | 8 | |
| β-strand | 2199-2204 | 6 | 8 |
| α-helix | 2209-2212 | 4 | |
| β-strand | 2222 | 1 | 8 |
| β-strand | 2231-2233 | 3 | 9 |
| β-strand | 2260-2262 | 3 | 9 |
| α-helix | 2268-2274 | 7 | |
| α-helix | 2280-2286 | 7 | |
| β-strand | 2288-2291 | 4 | 10 |
| β-strand | 2297-2301 | 5 | 10 |
| β-strand | 2310-2314 | 5 | 10 |
| α-helix | 2320-2333 | 14 | |
| β-strand | 2343-2346 | 4 | 10 |
| β-strand | 2351-2354 | 4 | 10 |
| β-strand | 2358-2360 | 3 | 10 |
| β-strand | 2364 | 1 | 11 |
| β-strand | 2368 | 1 | 11 |
Chain D: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27 | 1 | 12 |
| α-helix | 30-32 | 3 | |
| α-helix | 34-38 | 5 | |
| α-helix | 46-51 | 6 | |
| β-strand | 65 | 1 | 12 |
| α-helix | 66-74 | 9 | |
| α-helix | 82-92 | 11 | |
| β-strand | 101-102 | 2 | 13 |
| α-helix | 103-113 | 11 | |
| α-helix | 119-129 | 11 | |
| β-strand | 136-137 | 2 | 13 |
| α-helix | 140-146 | 7 | |
Chain E: 21 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1984 | 16 | |
| β-strand | 1992 | 1 | 14 |
| β-strand | 1995 | 1 | 14 |
| α-helix | 1997-1998 | 2 | |
| α-helix | 2010-2025 | 16 | |
| α-helix | 2034-2036 | 3 | |
| α-helix | 2037-2049 | 13 | |
| α-helix | 2052-2063 | 12 | |
| α-helix | 2074-2076 | 3 | |
| β-strand | 2077-2079 | 3 | 15 |
| β-strand | 2081-2082 | 2 | 16 |
| α-helix | 2087-2097 | 11 | |
| β-strand | 2103-2105 | 3 | 15 |
| α-helix | 2107-2109 | 3 | |
| α-helix | 2111-2129 | 19 | |
| α-helix | 2139-2161 | 23 | |
| β-strand | 2166-2171 | 6 | 16 |
| β-strand | 2176-2177 | 2 | 17 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2195 | 9 | |
| β-strand | 2199-2205 | 7 | 16 |
| α-helix | 2209-2212 | 4 | |
| α-helix | 2217-2219 | 3 | |
| β-strand | 2222 | 1 | 16 |
| β-strand | 2231-2233 | 3 | 17 |
| α-helix | 2240-2248 | 9 | |
| β-strand | 2260-2262 | 3 | 17 |
| α-helix | 2268-2273 | 6 | |
| α-helix | 2280-2286 | 7 | |
| β-strand | 2288-2292 | 5 | 18 |
| β-strand | 2297-2301 | 5 | 18 |
| β-strand | 2310-2314 | 5 | 18 |
| α-helix | 2320-2333 | 14 | |
| α-helix | 2337-2339 | 3 | |
| β-strand | 2343-2347 | 5 | 18 |
| β-strand | 2350-2354 | 5 | 18 |
| β-strand | 2358-2364 | 7 | 18 |
| β-strand | 2368-2370 | 3 | 18 |
Chain F: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27 | 1 | 19 |
| α-helix | 33-39 | 7 | |
| α-helix | 46-55 | 10 | |
| β-strand | 65 | 1 | 19 |
| α-helix | 66-78 | 13 | |
| α-helix | 82-91 | 10 | |
| β-strand | 100-102 | 3 | 20 |
| α-helix | 103-112 | 10 | |
| α-helix | 119-129 | 11 | |
| β-strand | 136-138 | 3 | 20 |
| α-helix | 139-144 | 6 | |
Chain G: 14 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1984 | 16 | |
| β-strand | 1998 | 1 | 21 |
| β-strand | 2001 | 1 | 21 |
| α-helix | 2010-2025 | 16 | |
| α-helix | 2036-2048 | 13 | |
| α-helix | 2052-2064 | 13 | |
| β-strand | 2077-2079 | 3 | 22 |
| β-strand | 2081-2082 | 2 | 23 |
| α-helix | 2087-2096 | 10 | |
| β-strand | 2103-2105 | 3 | 22 |
| α-helix | 2111-2128 | 18 | |
| α-helix | 2136-2161 | 26 | |
| β-strand | 2166-2171 | 6 | 23 |
| β-strand | 2176-2177 | 2 | 24 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2194 | 8 | |
| β-strand | 2199-2205 | 7 | 23 |
| α-helix | 2209-2212 | 4 | |
| β-strand | 2222 | 1 | 23 |
| β-strand | 2231-2233 | 3 | 24 |
| β-strand | 2260-2262 | 3 | 24 |
| α-helix | 2268-2274 | 7 | |
| α-helix | 2281-2286 | 6 | |
| β-strand | 2288-2292 | 5 | 25 |
| β-strand | 2297-2301 | 5 | 25 |
| β-strand | 2310-2314 | 5 | 25 |
| α-helix | 2320-2333 | 14 | |
| β-strand | 2343-2346 | 4 | 25 |
| β-strand | 2351-2354 | 4 | 25 |
| β-strand | 2358-2360 | 3 | 25 |
| β-strand | 2362-2364 | 3 | 26 |
| β-strand | 2368-2370 | 3 | 26 |
Chain H: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-17 | 11 | |
| β-strand | 27-28 | 2 | 27 |
| α-helix | 33-39 | 7 | |
| α-helix | 46-52 | 7 | |
| β-strand | 64-65 | 2 | 27 |
| α-helix | 66-76 | 11 | |
| α-helix | 82-91 | 10 | |
| β-strand | 101-102 | 2 | 28 |
| α-helix | 103-114 | 12 | |
| α-helix | 119-129 | 11 | |
| β-strand | 136-137 | 2 | 28 |
| α-helix | 139-146 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Rdtnd-rid cbd | A, C, E, G | protein | 416 | Vibrio vulnificus | A0A2S3R7M0 |
| Calmodulin-2 | B, D, F, H | protein | 151 | Homo sapiens | P0DP24 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>8KA1_1 RDTND-RID CBD (chains A, C, E, G)
GEASHDSAESLVAARAEKVANLYRWLDTDNDVATDKYVPVPGFERVDVDVSDEVKQRMIQ
SMSGYIEHTDNQVPKDQAEALATLFVESTLDYDWDKRVEFLTKLESYGYSFEAPHAEKSI
VSFWSGKNFKQYRDILDNAQTDGKKVVYDIDVKGNAFAIDLNKHLMRWGGLFLDPDNAEQ
NQLKSSIDAATFSNTGFWSSVYATGAQNDVYVIAEGGVRLGNYFWNVELPALRQLQREGL
VGEIRLLDKPVSEYKDLPADQIGRRLTDAGVAVKVRFDALSHERQAELLADNPDGYKADT
LVELDVKLSAIDSMLRESLPFYSLRTERNLLVQEGEEGFEVRSWPGIDGKSKTILLDNPE
DAAQQKSIERFILANFDNFEQMPDELFLVDNKVLSHHDGRTRIIAQKEDGAWTYNT
Sequence of entity 2 (B, D, F, H), FASTA
>8KA1_2 Calmodulin-2 (chains B, D, F, H)
GAMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDA
DGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT
DEEVDQMIREADIDGDGQVNYEEFVQMMTAK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 3 |
Primary citation
Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet. Choi, S., Lee, Y., Park, S. et al. Nat Commun (2024) 15:6218-6218. DOI 10.1038/s41467-024-50650-0 · PubMed
Other PDB entries of the same protein (UniProt A0A2S3R7M0), best resolution first:
- 8YJC 1.3 Å, Structure of Vibrio vulnificus MARTX cysteine protease domain C3727A
- 8YJA 2.2 Å, Structure of Vibrio vulnificus MARTX cysteine protease domain lacking beta-flap
- 8KA0 2.35 Å, Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain…
- 5XN7 2.7 Å, Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin
- 8K9Z 2.9 Å, Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain…
- 8KA2 3.38 Å, Crystal structure of the RID-dependent transforming NADase domain…
- 2N9W Solution NMR Structure of the membrane localization domain from the Ras/Rap1-specific…
Browse structure collections
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