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- PDB-1y0v: Crystal structure of anthrax edema factor (EF) in complex with ca... -

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Basic information

Entry
Database: PDB / ID: 1y0v
TitleCrystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate
Components
  • Calmodulin
  • Calmodulin-sensitive adenylate cyclase
KeywordsLYASE / Calcium-Independent / Calmodulin / Anthrax edema factor
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 / cAMP biosynthetic process / adenylate cyclase activity / myosin II complex / host cell cytosol / small molecule binding / Uptake and function of anthrax toxins ...symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / myosin II complex / host cell cytosol / small molecule binding / Uptake and function of anthrax toxins / catalytic complex / adenylate cyclase activator activity / metallopeptidase activity / toxin activity / calmodulin binding / signaling receptor binding / calcium ion binding / extracellular region / ATP binding / metal ion binding
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
PYROPHOSPHATE 2- / Calmodulin-1 / Calmodulin-sensitive adenylate cyclase / Calmodulin-2 B
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.6 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. / Tang, W.-J.
History
DepositionNov 16, 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 1.3Feb 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_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.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_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
H: Calmodulin
I: Calmodulin
J: Calmodulin
K: Calmodulin
L: Calmodulin
M: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)641,31342
Polymers639,39012
Non-polymers1,92330
Water00
1
A: Calmodulin-sensitive adenylate cyclase
H: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-50 kcal/mol
Surface area44350 Å2
MethodPISA
2
B: Calmodulin-sensitive adenylate cyclase
I: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-52 kcal/mol
Surface area44360 Å2
MethodPISA
3
C: Calmodulin-sensitive adenylate cyclase
J: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-51 kcal/mol
Surface area44390 Å2
MethodPISA
4
D: Calmodulin-sensitive adenylate cyclase
K: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-50 kcal/mol
Surface area44360 Å2
MethodPISA
5
E: Calmodulin-sensitive adenylate cyclase
L: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-50 kcal/mol
Surface area44330 Å2
MethodPISA
6
F: Calmodulin-sensitive adenylate cyclase
M: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8857
Polymers106,5652
Non-polymers3205
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-51 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)317.509, 183.348, 141.812
Angle α, β, γ (deg.)90.00, 90.05, 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase
#2: Protein
Calmodulin / CaM


Mass: 16436.053 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: CALM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62155, UniProt: P0DP33*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / 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: 2.1 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 375550 / Num. obs: 375293 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 77.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.063 / Net I/σ(I): 20
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9746 / Rsym value: 0.667 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.6→29.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 227881.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 4061 5 %RANDOM
Rwork0.286 ---
obs0.286 80945 86.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.206868 e/Å3
Displacement parametersBiso mean: 85.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å20 Å2
2---3.14 Å20 Å2
3---6.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-6 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.6→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42828 0 78 0 42906
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.482.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 499 5 %
Rwork0.331 9480 -
obs--63.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4PPI.PARAMPPI.TOP

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