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- PDB-8ka0: Crystal structure of Vibrio vulnificus RID-dependent transforming... -

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Basic information

Entry
Database: PDB / ID: 8ka0
TitleCrystal 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+)
Components
  • Calmodulin-2
  • RDTND-RID CBD
KeywordsTOXIN / MARTX toxin / RDTND-RID / NADase / CaM / NAD+
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / negative regulation of calcium ion transmembrane transporter activity / host cell cytosol / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / acyltransferase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / ligase activity ...Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / negative regulation of calcium ion transmembrane transporter activity / host cell cytosol / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / acyltransferase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / ligase activity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cysteine-type peptidase activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / positive regulation of protein serine/threonine kinase activity / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / toxin activity / vesicle / transmembrane transporter binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / G protein-coupled receptor signaling pathway / centrosome / lipid binding / calcium ion binding / protein kinase binding / host cell plasma membrane / protein-containing complex / proteolysis / extracellular region / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / : / Pasteurella multocida toxin, C2 domain / C-terminal repeat from RTX toxins / : / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain ...: / : / Pasteurella multocida toxin, C2 domain / C-terminal repeat from RTX toxins / : / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Multifunctional-autoprocessing repeats-in-toxin / Calmodulin-2
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLee, Y. / Choi, S. / Hwang, J. / Kim, M.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM1382312) Korea, Republic Of
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM2112335) Korea, Republic Of
CitationJournal: To Be Published
Title: 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 ...Title: 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+)
Authors: Lee, Y. / Choi, S. / Hwang, J. / Kim, M.H.
History
DepositionAug 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RDTND-RID CBD
B: Calmodulin-2
C: RDTND-RID CBD
D: Calmodulin-2
E: RDTND-RID CBD
F: Calmodulin-2
G: RDTND-RID CBD
H: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,63024
Polymers256,2878
Non-polymers3,34316
Water11,097616
1
A: RDTND-RID CBD
B: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8155
Polymers64,0722
Non-polymers7443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-47 kcal/mol
Surface area25330 Å2
MethodPISA
2
C: RDTND-RID CBD
D: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0007
Polymers64,0722
Non-polymers9285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-45 kcal/mol
Surface area25590 Å2
MethodPISA
3
E: RDTND-RID CBD
F: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0007
Polymers64,0722
Non-polymers9285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-48 kcal/mol
Surface area26020 Å2
MethodPISA
4
G: RDTND-RID CBD
H: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8155
Polymers64,0722
Non-polymers7443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-46 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.222, 48.931, 178.603
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
RDTND-RID CBD / MARTX


Mass: 47092.160 Da / Num. of mol.: 4 / Fragment: DUF1-RIDcbd (residues, 1959-2374) / Mutation: E2186Q
Source method: isolated from a genetically manipulated source
Details: NCBI accession ID: WP_015728045.1 / Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN52_02910 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2S3R7M0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein
Calmodulin-2


Mass: 16979.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal additional vector sequences, GA / Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP24

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Non-polymers , 4 types, 632 molecules

#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→29.62 Å / Num. obs: 98734 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 11.6
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 4831 / CC1/2: 0.675 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8K9Z

8k9z


Resolution: 2.35→29.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4996 5.1 %RANDOM
Rwork0.217 ---
obs0.22 93729 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-0.99 Å2
2---0.38 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17526 0 208 616 18350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01218076
X-RAY DIFFRACTIONr_bond_other_d0.0020.01616642
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.65124427
X-RAY DIFFRACTIONr_angle_other_deg0.7021.58238356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50852190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.6685116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.662103134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0490.22666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221536
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8145.5718792
X-RAY DIFFRACTIONr_mcbond_other4.8115.578792
X-RAY DIFFRACTIONr_mcangle_it7.34910.05410966
X-RAY DIFFRACTIONr_mcangle_other7.3510.05510967
X-RAY DIFFRACTIONr_scbond_it5.0496.0289284
X-RAY DIFFRACTIONr_scbond_other5.0496.0289285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.99610.8613462
X-RAY DIFFRACTIONr_long_range_B_refined11.75156.120362
X-RAY DIFFRACTIONr_long_range_B_other11.75156.120362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 361 -
Rwork0.3 6822 -
obs--99.87 %

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