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- PDB-1xfx: Crystal structure of anthrax edema factor (EF) in complex with ca... -

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Basic information

Entry
Database: PDB / ID: 1xfx
TitleCrystal structure of anthrax edema factor (EF) in complex with calmodulin in the presence of 10 millimolar exogenously added calcium chloride
Components
  • Calmodulin 2
  • Calmodulin-sensitive adenylate cyclase
KeywordsLYASE/METAL BINDING PROTEIN / protein-protein interaction / LYASE-METAL BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / : / : / : / : / : / adenylate cyclase / positive regulation of protein autophosphorylation ...symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / : / : / : / : / : / adenylate cyclase / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / cAMP biosynthetic process / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / adenylate cyclase activity / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / 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 / response to corticosterone / 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 / 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 / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase 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 / 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 / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability
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 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-sensitive adenylate cyclase / Calmodulin-3
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsShen, Y. / Zhukovskaya, N.L. / Guo, Q. / Florian, J. / Tang, W.J.
CitationJournal: EMBO J. / Year: 2005
Title: Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor.
Authors: Shen, Y. / Zhukovskaya, N.L. / Guo, Q. / Florian, J. / Tang, W.J.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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-sensitive adenylate cyclase
E: Calmodulin-sensitive adenylate cyclase
F: Calmodulin-sensitive adenylate cyclase
O: Calmodulin 2
P: Calmodulin 2
Q: Calmodulin 2
R: Calmodulin 2
S: Calmodulin 2
T: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,80442
Polymers644,69612
Non-polymers1,10830
Water00
1
A: Calmodulin-sensitive adenylate cyclase
O: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6347
Polymers107,4492
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-91 kcal/mol
Surface area43590 Å2
MethodPISA
2
B: Calmodulin-sensitive adenylate cyclase
P: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6347
Polymers107,4492
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-89 kcal/mol
Surface area43620 Å2
MethodPISA
3
C: Calmodulin-sensitive adenylate cyclase
Q: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6347
Polymers107,4492
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-90 kcal/mol
Surface area43610 Å2
MethodPISA
4
D: Calmodulin-sensitive adenylate cyclase
R: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6347
Polymers107,4492
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-75 kcal/mol
Surface area43580 Å2
MethodPISA
5
E: Calmodulin-sensitive adenylate cyclase
S: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6347
Polymers107,4492
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-88 kcal/mol
Surface area43570 Å2
MethodPISA
6
F: Calmodulin-sensitive adenylate cyclase
T: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6347
Polymers107,4492
Non-polymers1855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-91 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)318.303, 183.765, 141.516
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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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: 90128.898 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: cya / Production host: Escherichia coli (E. coli) / References: UniProt: P40136, adenylate cyclase
#2: Protein
Calmodulin 2


Mass: 17320.512 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 128111 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.038 / Rsym value: 0.025 / Net I/σ(I): 31
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.6 / Num. unique all: 132318 / Rsym value: 0.302 / % possible all: 95.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.2→17.45 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 239681.77 / 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
Rfree0.278 6479 5.1 %RANDOM
Rwork0.262 ---
obs0.262 128123 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.5762 Å2 / ksol: 0.201723 e/Å3
Displacement parametersBiso mean: 87.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 3.2→17.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42828 0 30 0 42858
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_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it1.372
X-RAY DIFFRACTIONc_scangle_it2.352.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.458 1019 5.2 %
Rwork0.42 18647 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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