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- PDB-6ynu: CaM-P458 complex (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 6ynu
TitleCaM-P458 complex (crystal form 1)
Components
  • Bifunctional adenylate cyclase toxin/hemolysin CyaA
  • Calmodulin-1
KeywordsMETAL BINDING PROTEIN / Toxin / CyaA
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / channel activity / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 ...calcium- and calmodulin-responsive adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / channel activity / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / myelin sheath / Ca2+ pathway / toxin activity / RAF/MAP kinase cascade / killing of cells of another organism
Similarity search - Function
Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX, pore-forming domain / N-terminal domain in RTX protein / 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 ...Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX, pore-forming domain / N-terminal domain in RTX protein / 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 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
Similarity search - Domain/homology
Cyclolysin / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsMechaly, A.E. / Voegele, A. / Haouz, A. / Chenal, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Adv Sci / Year: 2021
Title: A High-Affinity Calmodulin-Binding Site in the CyaA Toxin Translocation Domain is Essential for Invasion of Eukaryotic Cells.
Authors: Voegele, A. / Sadi, M. / O'Brien, D.P. / Gehan, P. / Raoux-Barbot, D. / Davi, M. / Hoos, S. / Brule, S. / Raynal, B. / Weber, P. / Mechaly, A. / Haouz, A. / Rodriguez, N. / Vachette, P. / ...Authors: Voegele, A. / Sadi, M. / O'Brien, D.P. / Gehan, P. / Raoux-Barbot, D. / Davi, M. / Hoos, S. / Brule, S. / Raynal, B. / Weber, P. / Mechaly, A. / Haouz, A. / Rodriguez, N. / Vachette, P. / Durand, D. / Brier, S. / Ladant, D. / Chenal, A.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
B: Bifunctional adenylate cyclase toxin/hemolysin CyaA
C: Calmodulin-1
D: Bifunctional adenylate cyclase toxin/hemolysin CyaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,80913
Polymers38,4484
Non-polymers3619
Water0
1
A: Calmodulin-1
hetero molecules

B: Bifunctional adenylate cyclase toxin/hemolysin CyaA


Theoretical massNumber of molelcules
Total (without water)19,4257
Polymers19,2242
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area1440 Å2
ΔGint-48 kcal/mol
Surface area11070 Å2
MethodPISA
2
C: Calmodulin-1
hetero molecules

D: Bifunctional adenylate cyclase toxin/hemolysin CyaA


Theoretical massNumber of molelcules
Total (without water)19,3856
Polymers19,2242
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area1480 Å2
ΔGint-54 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.341, 174.344, 97.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:

End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNchain 'A'AA3 - 1473 - 147
221GLNGLNchain 'C'CC3 - 1473 - 147
132TRPTRPchain 'B'BB458 - 4801 - 23
242TRPTRPchain 'D'DD458 - 4801 - 23

NCS ensembles :
ID
1
2

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Components

#1: Protein Calmodulin-1 /


Mass: 16721.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide Bifunctional adenylate cyclase toxin/hemolysin CyaA / Cyclolysin


Mass: 2502.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bordetella pertussis (bacteria) / References: UniProt: A0A380ZZA1
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 4.07 Å3/Da / Density % sol: 69.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion / Details: 0.3 M Ammonium sulfate 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.119→67.6 Å / Num. obs: 11538 / % possible obs: 99.49 % / Redundancy: 9 % / Biso Wilson estimate: 97.54 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.058 / Net I/σ(I): 22.97
Reflection shellResolution: 3.119→3.231 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 1132 / CC1/2: 0.946 / CC star: 0.986 / Rrim(I) all: 0.684

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CTR

1ctr


Resolution: 3.12→67.6 Å / SU ML: 0.3968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.9131
RfactorNum. reflection% reflection
Rfree0.2907 593 5.16 %
Rwork0.2463 --
obs0.2486 11495 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 147.89 Å2
Refinement stepCycle: LAST / Resolution: 3.12→67.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 9 0 2665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962684
X-RAY DIFFRACTIONf_angle_d1.14933606
X-RAY DIFFRACTIONf_chiral_restr0.0599398
X-RAY DIFFRACTIONf_plane_restr0.0077488
X-RAY DIFFRACTIONf_dihedral_angle_d1.85051638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.430.43191350.33932676X-RAY DIFFRACTION99.26
3.43-3.930.28911700.2342659X-RAY DIFFRACTION99.33
3.93-4.950.2551480.22472717X-RAY DIFFRACTION99.62
4.95-67.60.28771400.2442850X-RAY DIFFRACTION99.77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.360289145582.850268390892.898213230797.61553626371-1.147010032517.46412934367-0.2531278620070.886772878006-0.936882954060.2010420476320.476822830379-0.9711673235050.4961288737831.05686225119-0.3894365331820.7461215731570.065196688760.0385963983311.19854764726-0.02677877341440.916801702712-14.0612450119-44.834534511225.0656471931
22.659251485435.049483726767.724430837273.910708610066.011078897536.36703688880.9427191895990.548126395353-0.1770702225390.659111812094-0.7144082831390.02115336298380.856540309598-0.459800538614-0.3330142882851.03260914476-0.108826477321-0.07232773426771.53200413712-0.007204982330970.888625230427-28.9086251305-45.00859314715.9627257689
37.236437308040.7973588428863.532623796836.074879491090.277647585738.890018666070.06735308238841.98297121998-0.617880535563-0.432003718396-0.1966280697560.1293576197740.4305608850960.3090798267130.1232533203580.916613560620.236666274427-0.0004910049811971.31558750638-0.235572539460.811518453527-42.5743491822-53.215054279-1.28370162086
47.21089827142-2.986809269050.1979830476291.759429291132.798509187367.31381709365-0.00310100592505-1.035220011211.0198858557-0.3410216632760.3998856614880.098075200152-0.6061563622390.2028864154310.08565905890131.16316494834-0.0838054348168-0.08429579649140.71998212347-0.3493296634931.03092438925-46.0507015227-46.101766651113.3076196187
57.81098266682-1.24165902868-2.467921090512.29039387814-1.117718986565.48726036289-0.8916998345230.6525831379571.04953212190.4257167661531.60222428975-0.99177926166-0.8199782069030.0807209297193-0.6283121704961.20858700543-0.15217599242-0.1213474900131.802686131010.04812198131841.1616240097-52.3980916735-27.757383718326.9191936481
63.878908784981.80888346251-0.7552666164388.736692454070.9953397396296.61038064244-1.475425714460.6662231593441.92117820598-1.102859956480.1757682198921.89610275815-2.09319556238-0.2019679928870.8255284254511.509437044710.0363372942103-0.4915209560491.744743574620.5615574586562.25553327986-59.9217970613-16.304064023813.7462098378
70.00647540245393-0.01830560194940.00229028132290.00549203405589-0.0188292133889-0.000745649915624-0.6130606015730.74815496840.480594903346-1.44657085857-0.8309932490690.5980934672730.339382132492-1.027254340230.7900129797141.44664586216-0.429958404888-0.4612328630862.53335820265-0.101711892551.1665225273-61.8870410435-27.924272473910.6174146695
82.318980400876.77016828788-5.204517024265.63312742864-3.679102954673.4922368602-0.2836777634041.063076272511.07423721532-0.8695642895520.1531611712560.1121560419680.007692491469860.336420557277-0.02360909429941.11383362502-0.04982267765250.00856475735451.882197389950.1989593460721.17865646986-40.8817032464-21.063908851413.8563751494
96.923846716862.58189360597-0.9181728767175.5494534514-2.420437987725.415107610230.3379214886731.58092400309-0.0879561003659-1.269989399680.0672865327911-0.93564864707-0.4135263183280.048662310203-0.4287263578611.568964630080.00815006743610.1581750692221.582840331980.04635015201541.49454828885-22.7211417142-12.05340675242.06498025909
102.238272643720.02634910626941.350257973274.1547224472-3.054680073749.88835260026-0.546003411454-0.49004380387-0.72537324351-1.325145016380.687535726709-0.707235208541-1.96668311519-0.561392188938-0.1184431689591.426311384280.08092794489540.1622235939971.00531287938-0.1210885965611.67097881199-23.8258978941-19.805268438617.0886527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 148 )
4X-RAY DIFFRACTION4chain 'B' and (resid 458 through 481 )
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 19 )
6X-RAY DIFFRACTION6chain 'C' and (resid 20 through 55 )
7X-RAY DIFFRACTION7chain 'C' and (resid 56 through 64 )
8X-RAY DIFFRACTION8chain 'C' and (resid 65 through 92 )
9X-RAY DIFFRACTION9chain 'C' and (resid 93 through 148 )
10X-RAY DIFFRACTION10chain 'D' and (resid 458 through 481 )

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