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- PDB-1zot: crystal structure analysis of the CyaA/C-Cam with PMEAPP -

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Basic information

Entry
Database: PDB / ID: 1zot
Titlecrystal structure analysis of the CyaA/C-Cam with PMEAPP
Components
  • Calmodulin
  • CyaA with C-terminal Calmodulin
KeywordsLYASE / CyaA / adenylyl cyclase toxin / PMEapp / ATP / Calmodulin-binding
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / : / adenylate cyclase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation ...calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / : / adenylate cyclase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / channel activity / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis
Similarity search - Function
DNA polymerase; domain 1 - #920 / Alpha-Beta Plaits - #1720 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / : ...DNA polymerase; domain 1 - #920 / Alpha-Beta Plaits - #1720 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / : / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / : / EF-hand / Recoverin; domain 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. / DNA polymerase; domain 1 / EF-hand domain / EF-hand domain pair / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EMA / Bifunctional hemolysin/adenylate cyclase / Calmodulin-1 / Bifunctional hemolysin/adenylate cyclase / Calmodulin-3
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuo, Q. / Tang, W.J.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.
Authors: Guo, Q. / Shen, Y. / Lee, Y.S. / Gibbs, C.S. / Mrksich, M. / Tang, W.J.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CyaA with C-terminal Calmodulin
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1898
Polymers46,6032
Non-polymers5866
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-68 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.674, 79.674, 139.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CyaA with C-terminal Calmodulin


Mass: 38691.055 Da / Num. of mol.: 1 / Fragment: adenylyl cyclase toxin of Bordetella pertussis
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Plasmid: pProEx-H6-CyaA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pUBS520
References: UniProt: P15318, UniProt: P0DKX7*PLUS, adenylate cyclase
#2: Protein Calmodulin


Mass: 7911.559 Da / Num. of mol.: 1 / Fragment: C terminal calmodulin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pProEx-H6-CyaA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pUBS520 / References: UniProt: P62158, UniProt: P0DP23*PLUS

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Non-polymers , 4 types, 167 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EMA / (ADENIN-9-YL-ETHOXYMETHYL)-HYDROXYPHOSPHINYL-DIPHOSPHATE / 9-(2-PHOSPHONYLMETHOXYETHYL)ADENINE DIPHOSPHATE


Mass: 433.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N5O10P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, Na Citrate, Propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→34.5 Å / Num. all: 23504 / Num. obs: 21652 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 17.7 Å2
Reflection shellResolution: 2.2→2.34 Å / % possible all: 90.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.52 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 112331.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1068 4.9 %RANDOM
Rwork0.252 ---
obs0.252 21652 92.2 %-
all-23504 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.2051 Å2 / ksol: 0.316454 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2--2.71 Å20 Å2
3----4.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 31 161 3427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 170 4.9 %
Rwork0.303 3282 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4PMEApp.paramPMEApp.top

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