8KA0: 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+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+). Determined by X-ray diffraction at 2.35 Å resolution. Released 10 Jul 2024.
- Method
- X-ray diffraction
- Resolution
- 2.35 Å
- Organisms
- Vibrio vulnificus, Homo sapiens
- Chains
- 8
- Atoms
- 18,350
- Mol. weight
- 259.63 kDa
- Ligands
- NAD, CA
- Released
- 10 Jul 2024
Explore 8KA0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8KA0 contains 120 α-helices and 89 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: 22 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1984 | 16 | |
| α-helix | 1997 | 1 | |
| β-strand | 1998 | 1 | 1 |
| β-strand | 2001 | 1 | 1 |
| α-helix | 2010-2025 | 16 | |
| α-helix | 2036-2048 | 13 | |
| α-helix | 2052-2063 | 12 | |
| α-helix | 2074-2076 | 3 | |
| β-strand | 2077-2079 | 3 | 2 |
| β-strand | 2081-2083 | 3 | 3 |
| α-helix | 2087-2090 | 4 | |
| α-helix | 2091-2097 | 7 | |
| β-strand | 2103-2105 | 3 | 2 |
| α-helix | 2107-2109 | 3 | |
| α-helix | 2111-2129 | 19 | |
| α-helix | 2136-2161 | 26 | |
| β-strand | 2166-2172 | 7 | 3 |
| β-strand | 2176-2178 | 3 | 4 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2195 | 9 | |
| β-strand | 2199-2205 | 7 | 3 |
| α-helix | 2209-2212 | 4 | |
| α-helix | 2217-2219 | 3 | |
| β-strand | 2222 | 1 | 3 |
| β-strand | 2231-2234 | 4 | 4 |
| α-helix | 2235-2237 | 3 | |
| α-helix | 2240-2249 | 10 | |
| β-strand | 2259-2262 | 4 | 4 |
| α-helix | 2268-2276 | 9 | |
| α-helix | 2281-2286 | 6 | |
| β-strand | 2288-2293 | 6 | 5 |
| β-strand | 2296-2301 | 6 | 5 |
| β-strand | 2310-2314 | 5 | 5 |
| α-helix | 2320-2333 | 14 | |
| α-helix | 2337-2339 | 3 | |
| β-strand | 2343-2347 | 5 | 5 |
| β-strand | 2350-2355 | 6 | 5 |
| β-strand | 2357-2364 | 8 | 5 |
| β-strand | 2368-2370 | 3 | 5 |
Chain B: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27-29 | 3 | 6 |
| α-helix | 30-32 | 3 | |
| α-helix | 33-39 | 7 | |
| α-helix | 46-56 | 11 | |
| β-strand | 63-65 | 3 | 6 |
| α-helix | 66-79 | 14 | |
| α-helix | 82-91 | 10 | |
| β-strand | 100-102 | 3 | 7 |
| α-helix | 103-113 | 11 | |
| α-helix | 119-127 | 9 | |
| β-strand | 131 | 1 | 7 |
| β-strand | 136-138 | 3 | 7 |
| α-helix | 139-147 | 9 | |
Chain C: 23 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1984 | 16 | |
| α-helix | 1997 | 1 | |
| β-strand | 1998 | 1 | 8 |
| β-strand | 2001 | 1 | 8 |
| α-helix | 2010-2025 | 16 | |
| α-helix | 2036-2048 | 13 | |
| α-helix | 2052-2064 | 13 | |
| α-helix | 2074-2076 | 3 | |
| β-strand | 2077-2079 | 3 | 9 |
| β-strand | 2081-2083 | 3 | 10 |
| α-helix | 2087-2090 | 4 | |
| α-helix | 2091-2096 | 6 | |
| β-strand | 2103-2105 | 3 | 9 |
| α-helix | 2107-2109 | 3 | |
| α-helix | 2111-2129 | 19 | |
| α-helix | 2136-2161 | 26 | |
| β-strand | 2166-2172 | 7 | 10 |
| β-strand | 2176-2178 | 3 | 11 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2195 | 9 | |
| β-strand | 2199-2205 | 7 | 10 |
| α-helix | 2209-2212 | 4 | |
| α-helix | 2217-2219 | 3 | |
| β-strand | 2222 | 1 | 10 |
| β-strand | 2231-2234 | 4 | 11 |
| α-helix | 2235-2237 | 3 | |
| α-helix | 2240-2245 | 6 | |
| α-helix | 2246-2248 | 3 | |
| β-strand | 2259-2262 | 4 | 11 |
| α-helix | 2267-2274 | 8 | |
| α-helix | 2280-2286 | 7 | |
| β-strand | 2288-2291 | 4 | 12 |
| β-strand | 2297-2301 | 5 | 12 |
| β-strand | 2310-2314 | 5 | 12 |
| α-helix | 2320-2333 | 14 | |
| α-helix | 2337-2339 | 3 | |
| β-strand | 2343-2347 | 5 | 12 |
| β-strand | 2350-2354 | 5 | 12 |
| β-strand | 2358-2364 | 7 | 12 |
| β-strand | 2368-2370 | 3 | 12 |
Chain D: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27-28 | 2 | 13 |
| α-helix | 30-32 | 3 | |
| α-helix | 33-39 | 7 | |
| α-helix | 46-53 | 8 | |
| β-strand | 64-65 | 2 | 13 |
| α-helix | 66-79 | 14 | |
| α-helix | 82-91 | 10 | |
| β-strand | 100-102 | 3 | 14 |
| α-helix | 103-113 | 11 | |
| α-helix | 119-127 | 9 | |
| β-strand | 136-138 | 3 | 14 |
| α-helix | 139-147 | 9 | |
Chain E: 19 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1984 | 16 | |
| α-helix | 1997 | 1 | |
| β-strand | 1998 | 1 | 15 |
| β-strand | 2001 | 1 | 15 |
| α-helix | 2010-2025 | 16 | |
| α-helix | 2034-2036 | 3 | |
| α-helix | 2038-2049 | 12 | |
| α-helix | 2052-2064 | 13 | |
| β-strand | 2077-2079 | 3 | 16 |
| β-strand | 2081 | 1 | 17 |
| α-helix | 2091-2097 | 7 | |
| β-strand | 2103-2105 | 3 | 16 |
| α-helix | 2107-2109 | 3 | |
| α-helix | 2111-2130 | 20 | |
| α-helix | 2137-2161 | 25 | |
| β-strand | 2166-2171 | 6 | 17 |
| β-strand | 2176 | 1 | 18 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2195 | 9 | |
| β-strand | 2199-2205 | 7 | 17 |
| α-helix | 2217-2219 | 3 | |
| β-strand | 2222 | 1 | 17 |
| α-helix | 2229-2230 | 2 | |
| β-strand | 2231 | 1 | 18 |
| β-strand | 2232-2234 | 3 | 19 |
| β-strand | 2259-2261 | 3 | 19 |
| α-helix | 2262 | 1 | |
| α-helix | 2267-2276 | 10 | |
| α-helix | 2280-2286 | 7 | |
| β-strand | 2288-2292 | 5 | 20 |
| β-strand | 2297-2301 | 5 | 20 |
| β-strand | 2310-2314 | 5 | 20 |
| α-helix | 2320-2333 | 14 | |
| β-strand | 2343-2347 | 5 | 20 |
| β-strand | 2350-2355 | 6 | 20 |
| β-strand | 2357-2364 | 8 | 20 |
| β-strand | 2368-2370 | 3 | 20 |
Chain F: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-18 | 12 | |
| β-strand | 27-29 | 3 | 21 |
| α-helix | 30-32 | 3 | |
| α-helix | 33-39 | 7 | |
| α-helix | 46-56 | 11 | |
| β-strand | 63-65 | 3 | 21 |
| α-helix | 66-79 | 14 | |
| α-helix | 82-91 | 10 | |
| β-strand | 100-102 | 3 | 22 |
| α-helix | 103-113 | 11 | |
| α-helix | 119-127 | 9 | |
| β-strand | 136-138 | 3 | 22 |
| α-helix | 139-148 | 10 | |
Chain G: 20 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1969-1985 | 17 | |
| α-helix | 1997-1998 | 2 | |
| α-helix | 2012-2025 | 14 | |
| α-helix | 2036-2048 | 13 | |
| α-helix | 2052-2063 | 12 | |
| β-strand | 2077-2079 | 3 | 23 |
| β-strand | 2081 | 1 | 24 |
| α-helix | 2090-2096 | 7 | |
| β-strand | 2103-2105 | 3 | 23 |
| α-helix | 2107-2109 | 3 | |
| α-helix | 2111-2130 | 20 | |
| α-helix | 2137-2161 | 25 | |
| β-strand | 2166-2171 | 6 | 24 |
| β-strand | 2176 | 1 | 25 |
| α-helix | 2181 | 1 | |
| α-helix | 2182-2186 | 5 | |
| α-helix | 2187-2194 | 8 | |
| β-strand | 2199-2205 | 7 | 24 |
| α-helix | 2209-2212 | 4 | |
| α-helix | 2217-2219 | 3 | |
| β-strand | 2222 | 1 | 24 |
| α-helix | 2229-2230 | 2 | |
| β-strand | 2231-2234 | 4 | 25 |
| α-helix | 2235-2237 | 3 | |
| α-helix | 2240-2248 | 9 | |
| β-strand | 2259-2262 | 4 | 25 |
| α-helix | 2268-2276 | 9 | |
| α-helix | 2280-2286 | 7 | |
| β-strand | 2288-2292 | 5 | 26 |
| β-strand | 2297-2301 | 5 | 26 |
| β-strand | 2310-2314 | 5 | 26 |
| α-helix | 2320-2333 | 14 | |
| β-strand | 2343-2347 | 5 | 26 |
| β-strand | 2350-2354 | 5 | 26 |
| β-strand | 2358-2364 | 7 | 26 |
| β-strand | 2368-2370 | 3 | 26 |
Chain H: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 27-29 | 3 | 27 |
| α-helix | 30-32 | 3 | |
| α-helix | 33-39 | 7 | |
| α-helix | 46-56 | 11 | |
| β-strand | 63-65 | 3 | 27 |
| α-helix | 66-79 | 14 | |
| α-helix | 82-91 | 10 | |
| β-strand | 100-102 | 3 | 28 |
| α-helix | 103-113 | 11 | |
| α-helix | 119-128 | 10 | |
| β-strand | 132 | 1 | 28 |
| β-strand | 136-138 | 3 | 28 |
| α-helix | 139-147 | 9 | |
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
>8KA0_1 RDTND-RID CBD (chains A, C, E, G)
GEASHDSAESLVAARAEKVANLYRWLDTDNDVATDKYVPVPGFERVDVDVSDEVKQRMIQ
SMSGYIEHTDNQVPKDQAEALATLFVESTLDYDWDKRVEFLTKLESYGYSFEAPHAEKSI
VSFWSGKNFKQYRDILDNAQTDGKKVVYDIDVKGNAFAIDLNKHLMRWGGLFLDPDNAEQ
NQLKSSIDAATFSNTGFWSSVYATGAQNDVYVIAEGGVRLGNYFWNVQLPALRQLQREGL
VGEIRLLDKPVSEYKDLPADQIGRRLTDAGVAVKVRFDALSHERQAELLADNPDGYKADT
LVELDVKLSAIDSMLRESLPFYSLRTERNLLVQEGEEGFEVRSWPGIDGKSKTILLDNPE
DAAQQKSIERFILANFDNFEQMPDELFLVDNKVLSHHDGRTRIIAQKEDGAWTYNT
Sequence of entity 2 (B, D, F, H), FASTA
>8KA0_2 Calmodulin-2 (chains B, D, F, H)
GAMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDA
DGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT
DEEVDQMIREADIDGDGQVNYEEFVQMMTAK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAD | Nicotinamide-adenine-dinucleotide | C21 H27 N7 O14 P2 | 4 |
| CA | Calcium ion | Ca | 8 |
Water and common crystallization additives (GOL) are not listed.
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
- 5XN7 2.7 Å, Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin
- 8KA1 2.82 Å, Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain…
- 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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