9GR3 | pdb_00009gr3

The MK-RSL - sulfonato-calix[4]arene complex

PDB DOI: https://doi.org/10.2210/pdb9GR3/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-09-10 Released: 2025-03-05
Deposition Author(s): Mockler, N.M., Ramberg, K.O., Flood, R.J., Crowley, P.B.
Funding Organization(s): Irish Research Council, Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor.

Mockler, N.M., Ramberg, K.O., Flood, R.J., Crowley, P.B.

(2025) Biochemistry 64: 1092-1098

PubMed: 39977527 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.4c00729
Primary Citation of Related Structures:
9GR3, 9GR4, 9GR5

PubMed Abstract:
We describe the capture and structuring of disordered N-terminal regions by the macrocycle sulfonato-calix[4]arene ( sclx ₄). Using the trimeric β-propeller Ralstonia solanacearum lectin (RSL) as a scaffold, we generated a series of mutants with extended and dynamic N-termini. Three of the mutants feature an N-terminal methionine-lysine motif. The fourth mutant contains the disordered 8-residue N-terminus of Histone 3, a component of the nucleosome. X-ray crystallography and NMR spectroscopy provide evidence for sclx ₄ binding to the flexible N-terminal regions. Three crystal structures reveal that the calixarene recognizes the N-terminal Met-Lys motif, capturing either residue. We provide crystallographic proof for sclx ₄ encapsulation of N-terminal methionine. Calixarene capture of intrinsically disordered regions may have applications in regulating protein secondary (and tertiary) structure.

Organizational Affiliation

School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland.

Macromolecule Content

Total Structure Weight: 32.29 kDa
Atom Count: 2,600
Modelled Residue Count: 271
Deposited Residue Count: 273
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C	91	Ralstonia solanacearum	Mutation(s): 1 Gene Names: E7Z57_08365, HF909_06975, LBW55_09125, RUN39_v1_50103
UniProt
Find proteins for A0AAP7ZHZ3 (Ralstonia solanacearum K60) Explore A0AAP7ZHZ3 Go to UniProtKB: A0AAP7ZHZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAP7ZHZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T3Y (Subject of Investigation/LOI) Query on T3Y Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid C₂₈ H₂₄ O₁₆ S₄ JFYBCAFLVNKHHG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
BDF (Subject of Investigation/LOI) Query on BDF Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth C] E [auth A], F [auth A], H [auth B], I [auth B], J [auth C], K [auth C]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C]