7PR3

Cocrystal Form I of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster

PDB DOI: https://doi.org/10.2210/pdb7PR3/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-09-20 Released: 2022-03-02
Deposition Author(s): Flood, R.J., Ramberg, K., Guagnini, F., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland, Irish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.253
R-Value Work: 0.207
R-Value Observed: 0.210

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Protein Frameworks with Thiacalixarene and Zinc.

Flood, R.J., Ramberg, K.O., Mengel, D.B., Guagnini, F., Crowley, P.B.

(2022) Cryst Growth Des 22: 3271-3276

PubMed: 35529063 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.cgd.2c00108
Primary Citation of Related Structures:
7PR2, 7PR3, 7PR4, 7PR5

PubMed Abstract:
Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene ( tsclx ₄ ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx ₄ -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c ) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c , each involving multinuclear zinc sites supported by the cone conformation of tsclx ₄ . The tsclx ₄ /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx ₄ adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.

Organizational Affiliation

SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.

Macromolecule Content

Total Structure Weight: 58.27 kDa
Atom Count: 4,025
Modelled Residue Count: 428
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A, B, C, D	108	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044 Go to UniProtKB: P00044
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
80M (Subject of Investigation/LOI) Query on 80M Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain RA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain RA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain RA [auth D]	BA [auth C] G [auth A] H [auth A] N [auth B] O [auth B] BA [auth C], G [auth A], H [auth A], N [auth B], O [auth B], RA [auth D]	sulfonato-thiacalix[4]arene C₂₄ H₁₆ O₁₆ S₈ RUNCKYHXTXCYJH-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain RA [auth D] Interactions & Density Focus chain BA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain RA [auth D]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain MA [auth D] SDF format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain W [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain W [auth C]	E [auth A], L [auth B], MA [auth D], W [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain MA [auth D] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain MA [auth D] Focus chain W [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	AB [auth D] HA [auth C] IA [auth C] JA [auth C] YA [auth D] AB [auth D], HA [auth C], IA [auth C], JA [auth C], YA [auth D], ZA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AB [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain YA [auth D] Focus chain ZA [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth D] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth C] SDF format, chain TA [auth D] SDF format, chain U [auth C] SDF format, chain UA [auth D] SDF format, chain V [auth C] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain X [auth C] SDF format, chain XA [auth D] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] CA [auth C] DA [auth C] EA [auth C] F [auth A] AA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], GA [auth C], I [auth A], J [auth A], K [auth A], KA [auth D], LA [auth D], M [auth B], NA [auth D], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], S [auth B], SA [auth D], T [auth C], TA [auth D], U [auth C], UA [auth D], V [auth C], VA [auth D], WA [auth D], X [auth C], XA [auth D], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain M [auth B] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth C] Focus chain TA [auth D] Focus chain U [auth C] Focus chain UA [auth D] Focus chain V [auth C] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth C] Focus chain XA [auth D] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain M [auth B] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth C] Focus chain TA [auth D] Focus chain U [auth C] Focus chain UA [auth D] Focus chain V [auth C] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth C] Focus chain XA [auth D] Focus chain Y [auth C] Focus chain Z [auth C]