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- PDB-1lvc: Crystal structure of the adenylyl cyclase domain of anthrax edema... -

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Basic information

Entry
Database: PDB / ID: 1lvc
TitleCrystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP
Components
  • calmodulin
  • calmodulin-sensitive adenylate cyclase
KeywordsLYASE / helical domain / protein-protein complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / regulation of store-operated calcium channel activity / symbiont-mediated cAMP intoxication of host cell / regulation of high voltage-gated calcium channel activity / : / calcium- and calmodulin-responsive adenylate cyclase activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : ...symbiont-mediated perturbation of host signal transduction pathway / regulation of store-operated calcium channel activity / symbiont-mediated cAMP intoxication of host cell / regulation of high voltage-gated calcium channel activity / : / calcium- and calmodulin-responsive adenylate cyclase activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / adenylate cyclase / cAMP biosynthetic process / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / adenylate cyclase activity / establishment of protein localization to membrane / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / host cell cytosol / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / small molecule binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / presynaptic cytosol / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / voltage-gated potassium channel complex / regulation of calcium-mediated signaling / potassium ion transmembrane transport / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / response to amphetamine / calcium channel regulator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / nitric-oxide synthase regulator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #60 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / : / Oedema factor (EF), alpha-helical domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Anthrax toxin, lethal/endema factor ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #60 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / : / Oedema factor (EF), alpha-helical domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Anthrax toxin, lethal/endema factor / Anthrax toxin, lethal/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Metallopeptidase, catalytic domain superfamily / 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. / EF-hand domain / EF-hand domain pair / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3'ANTHRANILOYL-2'-DEOXY-ADENOSINE-5'-TRIPHOSPHATE / YTTERBIUM (III) ION / Calmodulin-1 / Calmodulin-1 / Calmodulin-sensitive adenylate cyclase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.6 Å
AuthorsShen, Y. / Lee, Y.-S. / Soelaiman, S. / Bergson, P. / Lu, D. / Chen, A. / Beckingham, K. / Grabarek, Z. / Mrksich, M. / Tang, W.-J.
Citation
Journal: Embo J. / Year: 2002
Title: Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins
Authors: Shen, Y. / Lee, Y.-S. / Soelaiman, S. / Bergson, P. / Lu, D. / Chen, A. / Beckingham, K. / Grabarek, Z. / Mrksich, M. / Tang, W.-J.
#1: Journal: Nature / Year: 2002
Title: Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
Authors: Drum, C.L. / Yan, S.Z. / Bard, J. / Shen, Y.Q. / Lu, D. / Soelaiman, S. / Grabarek, Z. / Bohm, A. / Tang, W.J.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conn
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: calmodulin-sensitive adenylate cyclase
B: calmodulin-sensitive adenylate cyclase
C: calmodulin-sensitive adenylate cyclase
D: calmodulin
E: calmodulin
F: calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,97017
Polymers226,9896
Non-polymers1,98011
Water00
1
A: calmodulin-sensitive adenylate cyclase
D: calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5276
Polymers75,6632
Non-polymers8634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-55 kcal/mol
Surface area30580 Å2
MethodPISA
2
B: calmodulin-sensitive adenylate cyclase
E: calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9165
Polymers75,6632
Non-polymers2533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-51 kcal/mol
Surface area32770 Å2
MethodPISA
3
C: calmodulin-sensitive adenylate cyclase
F: calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5276
Polymers75,6632
Non-polymers8634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-55 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.924, 167.918, 341.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is monomer

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Components

#1: Protein calmodulin-sensitive adenylate cyclase / ATP pyrophosphate-lyase / adenylyl cyclase / edema factor / ef / anthrax edema toxin adenylate ...ATP pyrophosphate-lyase / adenylyl cyclase / edema factor / ef / anthrax edema toxin adenylate cyclase component


Mass: 58810.605 Da / Num. of mol.: 3 / Fragment: c-terminal domain (residues 291-800)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Plasmid: pProEx / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase
#2: Protein calmodulin


Mass: 16852.545 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02593, UniProt: P0DP23*PLUS
#3: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-DOT / 3'ANTHRANILOYL-2'-DEOXY-ADENOSINE-5'-TRIPHOSPHATE


Mass: 610.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N6O13P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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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: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Details: Hiratsuka, T., (1983) Biochem. Biophys. Acta., 742, 496.

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→29.96 Å / Num. all: 39156 / Num. obs: 38841 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 10 / Num. unique all: 3871 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 3.6 Å / Redundancy: 6.85 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1K90

1k90


Resolution: 3.6→29.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 457541.92 / Data cutoff high rms absF: 457541.92 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1769 5 %RANDOM
Rwork0.281 ---
obs0.281 35570 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5231 Å2 / ksol: 0.25238 e/Å3
Displacement parametersBiso mean: 81.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.32 Å20 Å20 Å2
2--6.92 Å20 Å2
3----13.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.45 Å
Luzzati d res low-6 Å
Luzzati sigma a0.33 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.6→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15216 0 87 0 15303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.89
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it1.382
X-RAY DIFFRACTIONc_scangle_it2.432.5
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 272 5.3 %
Rwork0.302 4873 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ADA_XPLOR_PAR.TXTION.TOP
X-RAY DIFFRACTION4ION.PARAMADA_XPLOR_TOP.TXT
Refinement
*PLUS
Highest resolution: 3.6 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.89

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