1TZO | pdb_00001tzo

Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore

PDB DOI: https://doi.org/10.2210/pdb1TZO/pdb

Classification: TOXIN
Organism(s): Bacillus anthracis str. A2012
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-07-10 Released: 2004-08-17
Deposition Author(s): Lacy, D.B., Wigelsworth, D.J., Melnyk, R.A., Collier, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.317 (Depositor), 0.310 (DCC)
R-Value Work:
0.314 (Depositor), 0.307 (DCC)
R-Value Observed:
0.315 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of heptameric protective antigen bound to an anthrax toxin receptor: A role for receptor in pH-dependent pore formation

Lacy, D.B., Wigelsworth, D.J., Melnyk, R.A., Harrison, S.C., Collier, R.J.

(2004) Proc Natl Acad Sci U S A 101: 13147-13151

PubMed: 15326297 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0405405101
Primary Citation Related Structures:
1TZN, 1TZO

PubMed Abstract:
After binding to cellular receptors and proteolytic activation, the protective antigen component of anthrax toxin forms a heptameric prepore. The prepore later undergoes pH-dependent conversion to a pore, mediating translocation of the edema and lethal factors to the cytosol. We describe structures of the prepore (3.6 A) and a prepore:receptor complex (4.3 A) that reveal the location of pore-forming loops and an unexpected interaction of the receptor with the pore-forming domain. Lower pH is required for prepore-to-pore conversion in the presence of the receptor, indicating that this interaction regulates pH-dependent pore formation. We present an example of a receptor negatively regulating pH-dependent membrane insertion.

Organizational Affiliation

Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 883.39 kDa
Atom Count: 61,138
Modeled Residue Count: 7,742
Deposited Residue Count: 7,868
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protective antigen	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N [auth O]	562	Bacillus anthracis str. A2012	Mutation(s): 0 Gene Names: pagA
UniProt
Find proteins for P13423 (Bacillus anthracis) Explore P13423 Go to UniProtKB: P13423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13423
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain PA [auth O] SDF format, chain P [auth A] SDF format, chain OA [auth O] SDF format, chain O [auth A] SDF format, chain NA [auth M] SDF format, chain MA [auth M] SDF format, chain LA [auth L] SDF format, chain KA [auth L] SDF format, chain JA [auth K] SDF format, chain IA [auth K] SDF format, chain HA [auth J] SDF format, chain GA [auth J] SDF format, chain FA [auth I] SDF format, chain EA [auth I] SDF format, chain DA [auth H] SDF format, chain CA [auth H] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth O] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth O] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth M] MOL2 format, chain MA [auth M] MOL2 format, chain LA [auth L] MOL2 format, chain KA [auth L] MOL2 format, chain JA [auth K] MOL2 format, chain IA [auth K] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth J] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth I] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth O] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth O] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth M] mmCIF format, chain MA [auth M] mmCIF format, chain LA [auth L] mmCIF format, chain KA [auth L] mmCIF format, chain JA [auth K] mmCIF format, chain IA [auth K] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth J] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth I] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] CA [auth H] DA [auth H] EA [auth I] AA [auth G], BA [auth G], CA [auth H], DA [auth H], EA [auth I], FA [auth I], GA [auth J], HA [auth J], IA [auth K], JA [auth K], KA [auth L], LA [auth L], MA [auth M], NA [auth M], O [auth A], OA [auth O], P [auth A], PA [auth O], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D], V [auth D], W [auth E], X [auth E], Y [auth F], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain MA [auth M] Focus chain NA [auth M] Focus chain O [auth A] Focus chain OA [auth O] Focus chain P [auth A] Focus chain PA [auth O] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain MA [auth M] Focus chain NA [auth M] Focus chain O [auth A] Focus chain OA [auth O] Focus chain P [auth A] Focus chain PA [auth O] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.317 (Depositor), 0.310 (DCC)
R-Value Work: 0.314 (Depositor), 0.307 (DCC)
R-Value Observed: 0.315 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.608	α = 77.56
b = 167.028	β = 75.74
c = 168.2	γ = 76.01

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-08-17
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description