[English] 日本語
Yorodumi
- PDB-1k90: Crystal structure of the adenylyl cyclase domain of anthrax edema... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k90
TitleCrystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP
Components
  • CALMODULIN
  • CALMODULIN-SENSITIVE ADENYLATE CYCLASE
KeywordsTOXIN / LYASE/METAL BINDING PROTEIN / oedema factor adenylyl cyclase anthrax calmodulin / 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 / Calmodulin induced events / regulation of synaptic vesicle endocytosis / 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 / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / small molecule binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / adenylate cyclase binding / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / eNOS activation / Protein methylation / voltage-gated potassium channel complex / activation of adenylate cyclase activity / enzyme regulator activity / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / potassium ion transmembrane transport / nitric-oxide synthase regulator activity / substantia nigra development / adenylate cyclase activator activity / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of nitric-oxide synthase 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 / : / 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'-DEOXYADENOSINE-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 / MIR / Resolution: 2.75 Å
AuthorsDrum, C.L. / Yan, S.-Z. / Bard, J. / Shen, Y.-Q. / Lu, D. / Soelaiman, S. / Grabarek, Z. / Bohm, A. / Tang, W.-J.
CitationJournal: 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
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 7, 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

-
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)228,82918
Polymers226,5966
Non-polymers2,23312
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2766
Polymers75,5322
Non-polymers7444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-65 kcal/mol
Surface area30070 Å2
MethodPISA
3
C: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
F: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2766
Polymers75,5322
Non-polymers7444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-40 kcal/mol
Surface area30960 Å2
MethodPISA
4
B: CALMODULIN-SENSITIVE ADENYLATE CYCLASE
E: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2766
Polymers75,5322
Non-polymers7444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-63 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.099, 166.1, 343.33
Angle α, β, γ (deg.)90.0, 90.0, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 2 types, 6 molecules ABCDEF

#1: Protein CALMODULIN-SENSITIVE ADENYLATE CYCLASE


Mass: 58810.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase
#2: Protein CALMODULIN


Mass: 16721.350 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

-
Non-polymers , 4 types, 55 molecules

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


Mass: 173.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#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


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Ammonium Sulphate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 81651 / Num. obs: 81651 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.9 Å2
Reflection
*PLUS
% possible obs: 91.6 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 57.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.75→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 3888975.13 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 5
RfactorNum. reflection% reflectionSelection details
Rfree0.286 6625 10 %RANDOM
Rwork0.215 ---
obs0.215 74058 90.7 %-
all-81651 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8619 Å2 / ksol: 0.260013 e/Å3
Displacement parametersBiso mean: 90.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.2 Å20 Å20 Å2
2--15.75 Å20 Å2
3----9.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15215 0 99 43 15357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.75→2.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.446 1002 10 %
Rwork0.369 9049 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dtp_xplor.paramdtp_xplor.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 5 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 90.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
LS refinement shell
*PLUS
Rfactor Rfree: 0.446 / % reflection Rfree: 10 % / Rfactor Rwork: 0.369

+
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