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- PDB-1pk0: Crystal Structure of the EF3-CaM complexed with PMEApp -

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Basic information

Entry
Database: PDB / ID: 1pk0
TitleCrystal Structure of the EF3-CaM complexed with PMEApp
Components
  • Calmodulin-sensitive adenylate cyclase
  • Calmodulin
Keywordslyase/metal binding protein / edema factor / CaM / prodrug complex / lyase-metal binding protein COMPLEX
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / calmodulin dependent kinase signaling pathway / adenylate cyclase / : / establishment of protein localization to mitochondrial membrane / cAMP biosynthetic process / type 3 metabotropic glutamate receptor binding / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation ...calcium- and calmodulin-responsive adenylate cyclase activity / calmodulin dependent kinase signaling pathway / adenylate cyclase / : / establishment of protein localization to mitochondrial membrane / cAMP biosynthetic process / type 3 metabotropic glutamate receptor binding / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / host cell cytosol / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / 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 / regulation of synaptic vesicle exocytosis / 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 / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / 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 / small molecule binding / 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 / adenylate cyclase binding / 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 / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / 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 / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / 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 / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT
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 factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / 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
Chem-EMA / YTTERBIUM (III) ION / 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: 3.3 Å
AuthorsShen, Y. / Tang, W.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Selective inhibition of anthrax edema factor by adefovir, a drug for chronic hepatitis B virus infection.
Authors: Shen, Y. / Zhukovskaya, N.L. / Zimmer, M.I. / Soelaiman, S. / Bergson, P. / Wang, C.R. / Gibbs, C.S. / Tang, W.J.
#1: Journal: Embo J. / Year: 2002
Title: Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins
Authors: Shen, Y.-Q. / Lee, Y.-S. / Soelaiman, S. / Bergson, P. / Lu, D. / Chen, A. / Beckingham, K. / Grabarek, Z. / Mrksich, M. / Tang, W.-J.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 14, 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)227,14718
Polymers225,0886
Non-polymers2,05912
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Calmodulin-sensitive adenylate cyclase
F: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7166
Polymers75,0292
Non-polymers6864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-52 kcal/mol
Surface area31730 Å2
MethodPISA, PQS
3
A: Calmodulin-sensitive adenylate cyclase
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7166
Polymers75,0292
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-51 kcal/mol
Surface area30830 Å2
MethodPISA, PQS
4
B: Calmodulin-sensitive adenylate cyclase
E: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7166
Polymers75,0292
Non-polymers6864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-62 kcal/mol
Surface area32320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.263, 165.759, 342.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsBiological assembly is a monomer

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Components

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Protein , 2 types, 6 molecules ABCDEF

#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: 58437.215 Da / Num. of mol.: 3 / Fragment: residues 292-798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: CYA OR PXO1-122 / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / References: UniProt: P40136, adenylate cyclase
#2: Protein Calmodulin /


Mass: 16592.170 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: (CALM1 OR CAM1 OR CALM OR CAM) / Plasmid: pProEx / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS

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Non-polymers , 4 types, 29 molecules

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


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-EMA / (ADENIN-9-YL-ETHOXYMETHYL)-HYDROXYPHOSPHINYL-DIPHOSPHATE / 9-(2-PHOSPHONYLMETHOXYETHYL)ADENINE DIPHOSPHATE


Mass: 433.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H14N5O10P3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.66 Å3/Da / Density % sol: 66.43 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000,ammonium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal grow
*PLUS
Method: unknown / Details: Yan, S.Z., (2003) J.Biol.Chem., 278, 25990.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 49594 / Num. obs: 49594 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.88 % / Biso Wilson estimate: 51.7 Å2 / Rsym value: 0.094 / Net I/σ(I): 7.4
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.35 / Num. unique all: 4902 / Rsym value: 0.336 / % possible all: 99.8
Reflection
*PLUS
% possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: ef3-cam

Resolution: 3.3→14.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 372908.13 / 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
Rfree0.302 4766 10.1 %RANDOM
Rwork0.264 ---
all-49594 --
obs-47269 95.3 %-
Solvent computationSolvent model: flat model / Bsol: 25.8622 Å2 / ksol: 0.230872 e/Å3
Displacement parametersBiso mean: 72 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2--5.75 Å20 Å2
3----9.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-6 Å
Luzzati sigma a0.28 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 3.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15240 0 87 17 15344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.89
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.5 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 726 10 %
Rwork0.321 6544 -
obs--89 %
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 DIFFRACTION4PMEAPP.PARAMPMEAPP.TOP
Refinement
*PLUS
Highest resolution: 3.3 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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