6HSV | pdb_00006hsv

Engineered higher-order assembly of Cholera Toxin B subunits via the addition of C-terminal parallel coiled-coiled domains

PDB DOI: https://doi.org/10.2210/pdb6HSV/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-01 Released: 2019-03-20
Deposition Author(s): Pearson, A.R., Turnbull, W.B., Ross, J.F., Trinh, C.H., Webb, M.E.
Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council, German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.214 (Depositor), 0.213 (DCC)
R-Value Work:
0.195 (Depositor), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages.

Ross, J.F., Wildsmith, G.C., Johnson, M., Hurdiss, D.L., Hollingsworth, K., Thompson, R.F., Mosayebi, M., Trinh, C.H., Paci, E., Pearson, A.R., Webb, M.E., Turnbull, W.B.

(2019) J Am Chem Soc 141: 5211-5219

PubMed: 30856321 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.8b11480
Primary Citation Related Structures:
6HSV

PubMed Abstract:
The self-assembly of proteins into higher order structures is ubiquitous in living systems. It is also an essential process for the bottom-up creation of novel molecular architectures and devices for synthetic biology. However, the complexity of protein-protein interaction surfaces makes it challenging to mimic natural assembly processes in artificial systems. Indeed, many successful computationally designed protein assemblies are prescreened for "designability", limiting the choice of components. Here, we report a simple and pragmatic strategy to assemble chosen multisubunit proteins into more complex structures. A coiled-coil domain appended to one face of the pentameric cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular supra-molecular complexes. Analysis of a tubular structure determined by X-ray crystallography has revealed a hierarchical assembly process that displays features reminiscent of the polymorphic assembly of polyomavirus proteins. The approach provides a simple and straightforward method to direct the assembly of protein building blocks which present either termini on a single face of an oligomer. This scaffolding approach can be used to generate bespoke supramolecular assemblies of functional proteins. Additionally, structural resolution of the scaffolded assemblies highlight "native-state" forced protein-protein interfaces, which may prove useful as starting conformations for future computational design.

Organizational Affiliation

Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.

Macromolecule Content

Total Structure Weight: 281.39 kDa
Atom Count: 18,049
Modeled Residue Count: 2,237
Deposited Residue Count: 2,480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin B subunit	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	124	Vibrio cholerae	Mutation(s): 0 Gene Names: CTB
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P01556 Go to UniProtKB: P01556
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01556
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GA [auth H] SDF format, chain UA [auth Q] SDF format, chain VA [auth R] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain ZA [auth S] SDF format, chain YA [auth S] SDF format, chain XA [auth R] SDF format, chain WA [auth R] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain SA [auth P] SDF format, chain RA [auth P] SDF format, chain PA [auth O] SDF format, chain OA [auth O] SDF format, chain NA [auth N] SDF format, chain MA [auth M] SDF format, chain LA [auth L] SDF format, chain KA [auth J] SDF format, chain JA [auth J] SDF format, chain HA [auth H] SDF format, chain FA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain AB [auth T] SDF format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth H] MOL2 format, chain UA [auth Q] MOL2 format, chain VA [auth R] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth S] MOL2 format, chain YA [auth S] MOL2 format, chain XA [auth R] MOL2 format, chain WA [auth R] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain SA [auth P] MOL2 format, chain RA [auth P] MOL2 format, chain PA [auth O] MOL2 format, chain OA [auth O] MOL2 format, chain NA [auth N] MOL2 format, chain MA [auth M] MOL2 format, chain LA [auth L] MOL2 format, chain KA [auth J] MOL2 format, chain JA [auth J] MOL2 format, chain HA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain AB [auth T] MOL2 format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth H] mmCIF format, chain UA [auth Q] mmCIF format, chain VA [auth R] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth S] mmCIF format, chain YA [auth S] mmCIF format, chain XA [auth R] mmCIF format, chain WA [auth R] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain SA [auth P] mmCIF format, chain RA [auth P] mmCIF format, chain PA [auth O] mmCIF format, chain OA [auth O] mmCIF format, chain NA [auth N] mmCIF format, chain MA [auth M] mmCIF format, chain LA [auth L] mmCIF format, chain KA [auth J] mmCIF format, chain JA [auth J] mmCIF format, chain HA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain AB [auth T] mmCIF format, chain AA [auth D]	AA [auth D] AB [auth T] BA [auth D] DA [auth G] EA [auth G] AA [auth D], AB [auth T], BA [auth D], DA [auth G], EA [auth G], FA [auth H], GA [auth H], HA [auth H], JA [auth J], KA [auth J], LA [auth L], MA [auth M], NA [auth N], OA [auth O], PA [auth O], RA [auth P], SA [auth P], UA [auth Q], V [auth A], VA [auth R], W [auth A], WA [auth R], X [auth B], XA [auth R], Y [auth B], YA [auth S], ZA [auth S]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth T] Focus chain BA [auth D] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain LA [auth L] Focus chain MA [auth M] Focus chain NA [auth N] Focus chain OA [auth O] Focus chain PA [auth O] Focus chain RA [auth P] Focus chain SA [auth P] Focus chain UA [auth Q] Focus chain V [auth A] Focus chain VA [auth R] Focus chain W [auth A] Focus chain WA [auth R] Focus chain X [auth B] Focus chain XA [auth R] Focus chain Y [auth B] Focus chain YA [auth S] Focus chain ZA [auth S] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth T] Focus chain BA [auth D] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain LA [auth L] Focus chain MA [auth M] Focus chain NA [auth N] Focus chain OA [auth O] Focus chain PA [auth O] Focus chain RA [auth P] Focus chain SA [auth P] Focus chain UA [auth Q] Focus chain V [auth A] Focus chain VA [auth R] Focus chain W [auth A] Focus chain WA [auth R] Focus chain X [auth B] Focus chain XA [auth R] Focus chain Y [auth B] Focus chain YA [auth S] Focus chain ZA [auth S]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth A] SDF format, chain TA [auth Q] SDF format, chain QA [auth P] SDF format, chain IA [auth I] SDF format, chain CA [auth F] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth Q] MOL2 format, chain QA [auth P] MOL2 format, chain IA [auth I] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth Q] mmCIF format, chain QA [auth P] mmCIF format, chain IA [auth I] mmCIF format, chain CA [auth F]	CA [auth F] IA [auth I] QA [auth P] TA [auth Q] U [auth A] CA [auth F], IA [auth I], QA [auth P], TA [auth Q], U [auth A], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth F] Focus chain IA [auth I] Focus chain QA [auth P] Focus chain TA [auth Q] Focus chain U [auth A] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth F] Focus chain IA [auth I] Focus chain QA [auth P] Focus chain TA [auth Q] Focus chain U [auth A] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BB [auth T] MOL2 format, chain BB [auth T] mmCIF format, chain BB [auth T]	BB [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BB [auth T] Interactions & Density Focus chain BB [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.214 (Depositor), 0.213 (DCC)
R-Value Work: 0.195 (Depositor), 0.197 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.16	α = 90
b = 179.16	β = 90
c = 192.02	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	089308/Z/09/Z
Wellcome Trust	United Kingdom	102572/B/13/Z
Wellcome Trust	United Kingdom	090932/Z/09/Z
Wellcome Trust	United Kingdom	094232/Z/10/Z
Wellcome Trust	United Kingdom	108466/Z/15/Z
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M005666/1
German Research Foundation	Germany	EXC1074

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2019-04-10
Changes: Data collection, Database references
Version 1.2: 2019-05-08
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2019-07-10
Changes: Data collection
Version 1.4: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary

6HSV | pdb_00006hsv

Engineered higher-order assembly of Cholera Toxin B subunits via the addition of C-terminal parallel coiled-coiled domains

Literature

Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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