[English] 日本語
Yorodumi
- PDB-1xfw: Crystal structure of anthrax edema factor (EF) in complex with ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xfw
TitleCrystal structure of anthrax edema factor (EF) in complex with calmodulin and 3'5' cyclic AMP (cAMP)
Components
  • Calmodulin 2
  • Calmodulin-sensitive adenylate cyclase
KeywordsLYASE/METAL BINDING PROTEIN / protein-protein interaction / LYASE-METAL BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / calcium- and calmodulin-responsive adenylate cyclase activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / adenylate cyclase / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process ...symbiont-mediated perturbation of host signal transduction pathway / calcium- and calmodulin-responsive adenylate cyclase activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / adenylate cyclase / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / 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 / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / host cell cytosol / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / nitric-oxide synthase binding / response to corticosterone / positive regulation of DNA binding / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / negative regulation of peptidyl-threonine phosphorylation / calcineurin-mediated signaling / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of ryanodine-sensitive calcium-release channel activity / Phase 0 - rapid depolarisation / small molecule binding / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of synaptic vesicle endocytosis / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / protein phosphatase activator activity / adenylate cyclase binding / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of cardiac muscle contraction / detection of calcium ion / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / activation of adenylate cyclase activity / positive regulation of protein autophosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / positive regulation of peptidyl-threonine phosphorylation / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / FCERI mediated Ca+2 mobilization / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / regulation of heart rate / sarcomere / positive regulation of nitric-oxide synthase activity / protein serine/threonine kinase activator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Calmodulin-1 / Calmodulin-sensitive adenylate cyclase / Calmodulin-3
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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. / Florian, J. / Tang, W.J.
History
DepositionSep 15, 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 1.3Dec 20, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Feb 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_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_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

-
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-sensitive adenylate cyclase
E: Calmodulin-sensitive adenylate cyclase
F: Calmodulin-sensitive adenylate cyclase
O: Calmodulin 2
P: Calmodulin 2
Q: Calmodulin 2
R: Calmodulin 2
S: Calmodulin 2
T: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)644,72542
Polymers641,88312
Non-polymers2,84230
Water1086
1
A: Calmodulin-sensitive adenylate cyclase
O: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4547
Polymers106,9802
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-78 kcal/mol
Surface area44230 Å2
MethodPISA
2
B: Calmodulin-sensitive adenylate cyclase
P: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4547
Polymers106,9802
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-66 kcal/mol
Surface area44280 Å2
MethodPISA
3
C: Calmodulin-sensitive adenylate cyclase
Q: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4547
Polymers106,9802
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-66 kcal/mol
Surface area44250 Å2
MethodPISA
4
D: Calmodulin-sensitive adenylate cyclase
R: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4547
Polymers106,9802
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-79 kcal/mol
Surface area44280 Å2
MethodPISA
5
E: Calmodulin-sensitive adenylate cyclase
S: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4547
Polymers106,9802
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-65 kcal/mol
Surface area44230 Å2
MethodPISA
6
F: Calmodulin-sensitive adenylate cyclase
T: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4547
Polymers106,9802
Non-polymers4745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-79 kcal/mol
Surface area44260 Å2
MethodPISA
7
A: Calmodulin-sensitive adenylate cyclase
O: Calmodulin 2
hetero molecules

D: Calmodulin-sensitive adenylate cyclase
R: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,90814
Polymers213,9614
Non-polymers94710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area17020 Å2
ΔGint-167 kcal/mol
Surface area84540 Å2
MethodPISA
8
B: Calmodulin-sensitive adenylate cyclase
P: Calmodulin 2
hetero molecules

C: Calmodulin-sensitive adenylate cyclase
Q: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,90814
Polymers213,9614
Non-polymers94710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16890 Å2
ΔGint-141 kcal/mol
Surface area84530 Å2
MethodPISA
9
F: Calmodulin-sensitive adenylate cyclase
T: Calmodulin 2
hetero molecules

E: Calmodulin-sensitive adenylate cyclase
S: Calmodulin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,90814
Polymers213,9614
Non-polymers94710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_547-x+1/2,y-1/2,-z+21
Buried area16970 Å2
ΔGint-153 kcal/mol
Surface area84500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)320.501, 185.044, 142.454
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 12 molecules ABCDEFOPQRST

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P40136, adenylate cyclase
#2: Protein
Calmodulin 2


Mass: 16851.561 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS

-
Non-polymers , 4 types, 36 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N5O6P
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.98 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 28, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→100 Å / Num. obs: 106659 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.4 / Num. unique all: 120342 / Rsym value: 0.465 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→29.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 517178.02 / 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
Rfree0.283 5372 5 %RANDOM
Rwork0.266 ---
obs0.266 106659 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2411 Å2 / ksol: 0.26171 e/Å3
Displacement parametersBiso mean: 74.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.09 Å20 Å20.33 Å2
2---0.96 Å20 Å2
3---7.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.4→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42828 0 156 6 42990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.782.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 862 5.4 %
Rwork0.375 15006 -
obs--84 %
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 DIFFRACTION4CMP.PARAMCMP.TOP

+
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