[English] 日本語
Yorodumi
- PDB-1sk6: Crystal structure of the adenylyl cyclase domain of anthrax edema... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sk6
TitleCrystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin, 3',5' cyclic AMP (cAMP), and pyrophosphate
Components
  • Calmodulin
  • Calmodulin-sensitive adenylate cyclase
KeywordsToxin / Lyase/Metal Binding Protein / EF3 cAMP PPi CaM / Lyase-Metal Binding 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 / : / : / 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 / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / adenylate cyclase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / establishment of protein localization to membrane / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / host cell cytosol / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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 / CaMK IV-mediated phosphorylation of CREB / positive regulation of cyclic-nucleotide phosphodiesterase activity / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / adenylate cyclase binding / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / calcium channel regulator activity / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / small molecule binding / 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 / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / potassium ion transmembrane transport / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated potassium channel complex / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / PYROPHOSPHATE 2- / 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: 3.2 Å
AuthorsGuo, Q. / Shen, Y. / Zhukovskaya, N.L. / Tang, W.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate.
Authors: Guo, Q. / Shen, Y. / Zhukovskaya, N.L. / Florian, J. / Tang, W.J.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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_asym_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_asym_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_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
Remark 999SEQUENCE Residue (B ASN 521 ) and Residue (B GLU 524 ) are linked together. Residue (C PHE 773 ) ...SEQUENCE Residue (B ASN 521 ) and Residue (B GLU 524 ) are linked together. Residue (C PHE 773 ) and Residue (C LYS 774 ) are not linked, distance of C-N bond is 1.80.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)229,90927
Polymers226,5966
Non-polymers3,31321
Water00
1
A: Calmodulin-sensitive adenylate cyclase
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6369
Polymers75,5322
Non-polymers1,1047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-61 kcal/mol
Surface area30960 Å2
MethodPISA
2
B: Calmodulin-sensitive adenylate cyclase
E: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6369
Polymers75,5322
Non-polymers1,1047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-60 kcal/mol
Surface area32060 Å2
MethodPISA
3
C: Calmodulin-sensitive adenylate cyclase
F: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6369
Polymers75,5322
Non-polymers1,1047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-65 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.870, 166.453, 342.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
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: 58810.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: CYA, PXO1-122 / Plasmid: ProEx-H6-EF3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3 pUBS520 / References: UniProt: P40136, adenylate cyclase
#2: Protein Calmodulin


Mass: 16721.350 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02593, UniProt: P0DP23*PLUS

-
Non-polymers , 4 types, 21 molecules

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


Mass: 173.040 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N5O6P
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#6: 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: 3.95 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 50041 / Num. obs: 48122 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.13 / Net I/σ(I): 16.6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6739 / Rsym value: 0.484 / % possible all: 96.1

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1k90

1k90


Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3067 4829 -10%
Rwork0.2497 ---
all0.251 50041 --
obs0.2497 48122 96.2 %-
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14942 0 108 0 15050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0089
X-RAY DIFFRACTIONc_angle_deg1.34
LS refinement shellHighest resolution: 3.2 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.3067 4829 -
Rwork0.2497 --
obs-43293 96.5 %

+
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://pdbjlvh1.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