9DGH | pdb_00009dgh

Focused region on azoRhuA-bCDRhuA co-assembled nanotubes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design of light- and chemically responsive protein assemblies through host-guest interactions.

Zhang, Z.Chiang, H.T.Xia, Y.Avakyan, N.Sonani, R.R.Wang, F.Egelman, E.H.De Yoreo, J.J.Pozzo, L.D.Tezcan, F.A.

(2025) Chem 11

  • DOI: https://doi.org/10.1016/j.chempr.2024.102407
  • Primary Citation of Related Structures:  
    9DGH

  • PubMed Abstract: 

    Host-guest interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse stimuli. Here we have set out to exploit these advantages of host-guest chemistry in the design of dynamic protein assemblies, using a C 4 symmetric protein, C98 RhuA, as a building block. We show that C98 RhuA variant individually modified with β-cyclodextrin (βCD) (host) or azobenzene (guest) functionalities can specifically pair with each other to form highly ordered 1- and 2-D assemblies. Association and dissociation βCD RhuA- azo RhuA assemblies can be controlled by UV and visible light as well as by small-molecule modulators of βCD-azobenzene interactions. Kinetics analyses reveal that βCD RhuA- azo RhuA nanotubes assemble without a nucleation barrier, a highly unusual occurrence for helical supramolecular systems. Taken together, our findings provide a compelling example for achieving complex structural and dynamic outcomes in protein assembly through simple chemical design.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhamnulose-1-phosphate aldolase274Escherichia coliMutation(s): 0 
Gene Names: rhaDrhuAb3902JW3873
EC: 4.1.2.19
UniProt
Find proteins for P32169 (Escherichia coli (strain K12))
Explore P32169 
Go to UniProtKB:  P32169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32169
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)-alpha-D-glucopyranose
Q, R
7N/A
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A4G
Query on A1A4G

Download Ideal Coordinates CCD File 
CA [auth I],
Y [auth H]
1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione
C16 H15 N3 O2
XQZVOVPQWDSFBG-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth I]
DA [auth L]
EA [auth J]
FA [auth K]
AA [auth G],
BA [auth I],
DA [auth L],
EA [auth J],
FA [auth K],
GA [auth M],
HA [auth P],
IA [auth N],
JA [auth O],
S [auth A],
T [auth D],
U [auth B],
V [auth C],
W [auth E],
X [auth H],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Data collection, Database references