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- PDB-1tzn: Crystal Structure of the Anthrax Toxin Protective Antigen Heptame... -

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Basic information

Entry
Database: PDB / ID: 1tzn
TitleCrystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore bound to the VWA domain of CMG2, an anthrax toxin receptor
Components
  • Anthrax toxin receptor 2
  • Protective antigen
KeywordsTOXIN RECEPTOR/TOXIN / heptamer / TOXIN RECEPTOR-TOXIN COMPLEX
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / transmembrane signaling receptor activity / toxin activity / endosome membrane / endoplasmic reticulum membrane ...positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / transmembrane signaling receptor activity / toxin activity / endosome membrane / endoplasmic reticulum membrane / host cell plasma membrane / cell surface / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain ...Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Protective antigen / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsLacy, D.B. / Wigelsworth, D.J. / Melnyk, R.A. / Collier, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of heptameric protective antigen bound to an anthrax toxin receptor: A role for receptor in pH-dependent pore formation
Authors: Lacy, D.B. / Wigelsworth, D.J. / Melnyk, R.A. / Harrison, S.C. / Collier, R.J.
History
DepositionJul 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 3, 2024Group: 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_asym_id / _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.ptnr3_auth_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protective antigen
a: Anthrax toxin receptor 2
B: Protective antigen
b: Anthrax toxin receptor 2
C: Protective antigen
c: Anthrax toxin receptor 2
D: Protective antigen
d: Anthrax toxin receptor 2
E: Protective antigen
e: Anthrax toxin receptor 2
F: Protective antigen
f: Anthrax toxin receptor 2
G: Protective antigen
g: Anthrax toxin receptor 2
H: Protective antigen
h: Anthrax toxin receptor 2
I: Protective antigen
i: Anthrax toxin receptor 2
J: Protective antigen
j: Anthrax toxin receptor 2
K: Protective antigen
k: Anthrax toxin receptor 2
L: Protective antigen
l: Anthrax toxin receptor 2
M: Protective antigen
m: Anthrax toxin receptor 2
O: Protective antigen
o: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,161,50070
Polymers1,160,03728
Non-polymers1,46242
Water00
1
A: Protective antigen
a: Anthrax toxin receptor 2
B: Protective antigen
b: Anthrax toxin receptor 2
C: Protective antigen
c: Anthrax toxin receptor 2
D: Protective antigen
d: Anthrax toxin receptor 2
E: Protective antigen
e: Anthrax toxin receptor 2
F: Protective antigen
f: Anthrax toxin receptor 2
O: Protective antigen
o: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)580,75035
Polymers580,01914
Non-polymers73121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41440 Å2
ΔGint-175 kcal/mol
Surface area212150 Å2
MethodPISA
2
G: Protective antigen
g: Anthrax toxin receptor 2
H: Protective antigen
h: Anthrax toxin receptor 2
I: Protective antigen
i: Anthrax toxin receptor 2
J: Protective antigen
j: Anthrax toxin receptor 2
K: Protective antigen
k: Anthrax toxin receptor 2
L: Protective antigen
l: Anthrax toxin receptor 2
M: Protective antigen
m: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)580,75035
Polymers580,01914
Non-polymers73121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41500 Å2
ΔGint-176 kcal/mol
Surface area212100 Å2
MethodPISA
3
A: Protective antigen
a: Anthrax toxin receptor 2
B: Protective antigen
b: Anthrax toxin receptor 2
C: Protective antigen
c: Anthrax toxin receptor 2
D: Protective antigen
d: Anthrax toxin receptor 2
E: Protective antigen
e: Anthrax toxin receptor 2
F: Protective antigen
f: Anthrax toxin receptor 2
O: Protective antigen
o: Anthrax toxin receptor 2
hetero molecules

G: Protective antigen
g: Anthrax toxin receptor 2
H: Protective antigen
h: Anthrax toxin receptor 2
I: Protective antigen
i: Anthrax toxin receptor 2
J: Protective antigen
j: Anthrax toxin receptor 2
K: Protective antigen
k: Anthrax toxin receptor 2
L: Protective antigen
l: Anthrax toxin receptor 2
M: Protective antigen
m: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,161,50070
Polymers1,160,03728
Non-polymers1,46242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area83520 Å2
ΔGint-350 kcal/mol
Surface area423680 Å2
MethodPISA
4
A: Protective antigen
a: Anthrax toxin receptor 2
B: Protective antigen
b: Anthrax toxin receptor 2
C: Protective antigen
c: Anthrax toxin receptor 2
D: Protective antigen
d: Anthrax toxin receptor 2
E: Protective antigen
e: Anthrax toxin receptor 2
F: Protective antigen
f: Anthrax toxin receptor 2
O: Protective antigen
o: Anthrax toxin receptor 2
hetero molecules

G: Protective antigen
g: Anthrax toxin receptor 2
H: Protective antigen
h: Anthrax toxin receptor 2
I: Protective antigen
i: Anthrax toxin receptor 2
J: Protective antigen
j: Anthrax toxin receptor 2
K: Protective antigen
k: Anthrax toxin receptor 2
L: Protective antigen
l: Anthrax toxin receptor 2
M: Protective antigen
m: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,161,50070
Polymers1,160,03728
Non-polymers1,46242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area88780 Å2
ΔGint-344 kcal/mol
Surface area418420 Å2
MethodPISA
5
A: Protective antigen
a: Anthrax toxin receptor 2
B: Protective antigen
b: Anthrax toxin receptor 2
C: Protective antigen
c: Anthrax toxin receptor 2
D: Protective antigen
d: Anthrax toxin receptor 2
E: Protective antigen
e: Anthrax toxin receptor 2
F: Protective antigen
f: Anthrax toxin receptor 2
O: Protective antigen
o: Anthrax toxin receptor 2
hetero molecules

G: Protective antigen
g: Anthrax toxin receptor 2
H: Protective antigen
h: Anthrax toxin receptor 2
I: Protective antigen
i: Anthrax toxin receptor 2
J: Protective antigen
j: Anthrax toxin receptor 2
K: Protective antigen
k: Anthrax toxin receptor 2
L: Protective antigen
l: Anthrax toxin receptor 2
M: Protective antigen
m: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,161,50070
Polymers1,160,03728
Non-polymers1,46242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_544x,y-1,z-11
Buried area84170 Å2
ΔGint-346 kcal/mol
Surface area423030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.800, 158.846, 214.084
Angle α, β, γ (deg.)69.58, 69.07, 65.58
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsThe biological assembly is one heptamer

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Components

#1: Protein
Protective antigen / pXO1-110 / PA-83 / PA83


Mass: 63019.012 Da / Num. of mol.: 14 / Fragment: 63-kDa domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: A2012 / Gene: pagA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3 Star / References: UniProt: P13423
#2: Protein
Anthrax toxin receptor 2 / capillary morphogenesis protein 2 / CMG-2


Mass: 19840.791 Da / Num. of mol.: 14 / Fragment: VWA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3 Star / References: UniProt: P58335
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg

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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: 3.8 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, sodium chloride, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2004 / Details: null
RadiationMonochromator: horizontally bent Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 4.3→20 Å / Num. all: 120016 / Num. obs: 120016 / % possible obs: 97.3 % / Observed criterion σ(I): 1.8 / Redundancy: 2.7 % / Rsym value: 0.165 / Net I/σ(I): 6.8
Reflection shellResolution: 4.3→4.45 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 12124 / Rsym value: 0.449 / % possible all: 98.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3.6 heptameric prepore model

Resolution: 4.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.33 5704 -random
Rwork0.322 ---
all0.3251 116356 --
obs0.325 113061 97.2 %-
Refinement stepCycle: LAST / Resolution: 4.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms80528 0 42 0 80570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9

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