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- PDB-1k90: Crystal structure of the adenylyl cyclase domain of anthrax edema... -

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Basic information

Entry
Database: PDB / ID: 1k90
TitleCrystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP
Components
  • CALMODULIN
  • CALMODULIN-SENSITIVE ADENYLATE CYCLASE
KeywordsTOXIN / LYASE/METAL BINDING PROTEIN / oedema factor adenylyl cyclase anthrax calmodulin / LYASE-METAL BINDING 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 / : / : / 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 / : / : / calcium- and calmodulin-responsive adenylate cyclase activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / : / : / : / 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 / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / host cell cytosol / 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 / 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 / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / small molecule binding / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / response to amphetamine / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation
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'-DEOXYADENOSINE-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 / MIR / Resolution: 2.75 Å
AuthorsDrum, C.L. / Yan, S.-Z. / Bard, J. / Shen, Y.-Q. / Lu, D. / Soelaiman, S. / Grabarek, Z. / Bohm, A. / Tang, W.-J.
CitationJournal: 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
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / struct_conn
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
D: CALMODULIN
B: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
E: CALMODULIN
C: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
F: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,82918
Polymers226,5966
Non-polymers2,23312
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2766
Polymers75,5322
Non-polymers7444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-65 kcal/mol
Surface area30070 Å2
MethodPISA
3
C: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
F: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2766
Polymers75,5322
Non-polymers7444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-40 kcal/mol
Surface area30960 Å2
MethodPISA
4
B: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
E: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2766
Polymers75,5322
Non-polymers7444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-63 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.099, 166.1, 343.33
Angle α, β, γ (deg.)90.0, 90.0, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein CALMODULIN-SENSITIVE ADENYLATE CYCLASE


Mass: 58810.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase
#2: Protein CALMODULIN


Mass: 16721.350 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

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Non-polymers , 4 types, 55 molecules

#3: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Ammonium Sulphate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 81651 / Num. obs: 81651 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.9 Å2
Reflection
*PLUS
% possible obs: 91.6 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 57.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.75→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 3888975.13 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 5
RfactorNum. reflection% reflectionSelection details
Rfree0.286 6625 10 %RANDOM
Rwork0.215 ---
obs0.215 74058 90.7 %-
all-81651 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8619 Å2 / ksol: 0.260013 e/Å3
Displacement parametersBiso mean: 90.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.2 Å20 Å20 Å2
2--15.75 Å20 Å2
3----9.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15215 0 99 43 15357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
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: 2.75→2.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.446 1002 10 %
Rwork0.369 9049 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dtp_xplor.paramdtp_xplor.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 5 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 90.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
LS refinement shell
*PLUS
Rfactor Rfree: 0.446 / % reflection Rfree: 10 % / Rfactor Rwork: 0.369

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