8K9Z: Rdtnd-rid cbd

Name: PDB 8K9Z: 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
Published: 2024-07-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

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. Determined by X-ray diffraction at 2.9 Å resolution. Released 10 Jul 2024.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Vibrio vulnificus, Homo sapiens
Chains: 4
Atoms: 8,608
Mol. weight: 126.2 kDa
Ligands: CA
Released: 10 Jul 2024

Explore 8K9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K9Z contains 55 α-helices and 44 β-strands across 4 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	1969-1984	16
α-helix	1997-1998	2
α-helix	2013-2026	14
α-helix	2033-2035	3
α-helix	2036-2048	13
α-helix	2052-2065	14
β-strand	2077-2079	3	1
β-strand	2081-2082	2	2
α-helix	2087-2096	10
β-strand	2103-2105	3	1
α-helix	2107-2109	3
α-helix	2111-2130	20
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	2231-2234	4	3
α-helix	2240-2245	6
β-strand	2259-2262	4	3
α-helix	2266-2276	11
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	2350-2354	5	4
β-strand	2358-2364	7	4
β-strand	2368-2369	2	4

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-28	2	5
α-helix	33-38	6
α-helix	48-56	9
β-strand	64-65	2	5
α-helix	66-79	14
α-helix	82-91	10
β-strand	95	1	6
β-strand	97	1	6
β-strand	100-101	2	7
α-helix	103-113	11
α-helix	119-127	9
β-strand	137-138	2	7
α-helix	139-146	8

Chain C: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	1969-1983	15
β-strand	1992	1	8
β-strand	1995	1	8
α-helix	2007-2009	3
α-helix	2010-2025	16
α-helix	2033-2035	3
α-helix	2036-2048	13
α-helix	2052-2063	12
α-helix	2074-2076	3
β-strand	2078-2079	2	9
β-strand	2081-2082	2	10
α-helix	2087-2091	5
β-strand	2104-2105	2	9
α-helix	2111-2129	19
α-helix	2139-2161	23
β-strand	2166-2171	6	10
β-strand	2176-2177	2	11
α-helix	2181	1
α-helix	2182-2186	5
α-helix	2187-2195	9
β-strand	2199-2205	7	10
α-helix	2209-2211	3
β-strand	2222	1	10
β-strand	2231-2233	3	11
β-strand	2260-2262	3	11
α-helix	2267-2276	10
α-helix	2280-2286	7
β-strand	2288-2292	5	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	2358-2363	6	12
β-strand	2369-2370	2	12

Chain D: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-29	3	13
α-helix	33-38	6
α-helix	46-56	11
β-strand	63-65	3	13
α-helix	66-75	10
α-helix	82-88	7
α-helix	91-93	3
β-strand	100-102	3	14
α-helix	103-113	11
α-helix	119-129	11
β-strand	136-138	3	14
α-helix	139-146	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rdtnd-rid cbd	A, C	protein	405	Vibrio vulnificus	A0A2S3R7M0
Calmodulin-2	B, D	protein	151	Homo sapiens	P0DP24 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8K9Z_1 RDTND-RID CBD (chains A, C)
ESLVAARAEKVANLYRWLDTDNDVATDKYVPVPGFERVDVDVSDEVKQRMIQSMSGYIEH
TDNQVPKDQAEALATLFVESTLDYDWDKRVEFLTKLESYGYSFEAPHAEKSIVSFWSGKN
FKQYRDILDNAQTDGKKVVYDIDVKGNAFAIDLNKHLMRWGGLFLDPDNAEQNQLKSSID
AATFSNTGFWSSVYATGAQNDVYVIAEGGVRLGNYFWNVELPALRQLQREGLVGEIRLLD
KPVSEYKDLPADQIGRRLTDAGVAVKVRFDALSHERQAELLADNPDGYKADTLVELDVKL
SAIDSMLRESLPFYSLRTERNLLVQEGEEGFEVRSWPGIDGKSKTILLDNPEDAAQQKSI
ERFILANFDNFEQMPDELFLVDNKVLSHHDGRTRIIAQKEDGAWT

Sequence of entity 2 (B, D), FASTA

>8K9Z_2 Calmodulin-2 (chains B, D)
GAMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDA
DGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT
DEEVDQMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8

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
8KA1 2.82 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

About this viewer

MolViewer shows 8K9Z directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.