[English] 日本語
Yorodumi
- PDB-1lvc: Crystal structure of the adenylyl cyclase domain of anthrax edema... -

+
Open data


ID or keywords:

Loading...

-
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-sensitive adenylate cyclase
  • calmodulin
KeywordsLYASE / helical domain / protein-protein complex
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / calcium- and calmodulin-responsive adenylate cyclase activity / calmodulin dependent kinase signaling pathway / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / adenylate cyclase / : ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / calcium- and calmodulin-responsive adenylate cyclase activity / calmodulin dependent kinase signaling pathway / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / adenylate cyclase / : / establishment of protein localization to mitochondrial membrane / cAMP biosynthetic process / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / 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 / 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 / calcium channel regulator activity / 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 / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / 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 / potassium ion transmembrane transport / 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
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / Ytterbium


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more