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- PDB-9dgh: Focused region on azoRhuA-bCDRhuA co-assembled nanotubes -

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Basic information

Entry
Database: PDB / ID: 9dgh
TitleFocused region on azoRhuA-bCDRhuA co-assembled nanotubes
ComponentsRhamnulose-1-phosphate aldolase
KeywordsLYASE / Assembly
Function / homology
Function and homology information


rhamnulose-1-phosphate aldolase / rhamnulose-1-phosphate aldolase activity / rhamnose catabolic process / pentose catabolic process / aldehyde-lyase activity / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Rhamnulose-1-phosphate aldolase / : / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily
Similarity search - Domain/homology
: / Rhamnulose-1-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhang, Z. / Sonani, R.R. / Wang, F. / Egelman, E.H. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Chem / Year: 2025
Title: Design of light- and chemically responsive protein assemblies through host-guest interactions.
Authors: Zhiyin Zhang / Huat T Chiang / Ying Xia / Nicole Avakyan / Ravi R Sonani / Fengbin Wang / Edward H Egelman / James J De Yoreo / Lilo D Pozzo / F Akif Tezcan /
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 ...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 symmetric protein, RhuA, as a building block. We show that 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 RhuA-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 RhuA-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.
History
DepositionSep 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhamnulose-1-phosphate aldolase
D: Rhamnulose-1-phosphate aldolase
B: Rhamnulose-1-phosphate aldolase
C: Rhamnulose-1-phosphate aldolase
E: Rhamnulose-1-phosphate aldolase
H: Rhamnulose-1-phosphate aldolase
F: Rhamnulose-1-phosphate aldolase
G: Rhamnulose-1-phosphate aldolase
I: Rhamnulose-1-phosphate aldolase
L: Rhamnulose-1-phosphate aldolase
J: Rhamnulose-1-phosphate aldolase
K: Rhamnulose-1-phosphate aldolase
M: Rhamnulose-1-phosphate aldolase
P: Rhamnulose-1-phosphate aldolase
N: Rhamnulose-1-phosphate aldolase
O: Rhamnulose-1-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,38536
Polymers481,41416
Non-polymers3,97120
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Rhamnulose-1-phosphate aldolase


Mass: 30088.361 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rhaD, rhuA, b3902, JW3873 / Production host: Escherichia coli (E. coli)
References: UniProt: P32169, rhamnulose-1-phosphate aldolase
#2: Polysaccharide Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)- ...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


Type: oligosaccharide / Mass: 1180.967 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,7,7/[a2122h-1a_1-5][a2122A-1a_1-5]/1-1-1-2-1-1-2/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1A4G / 1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione


Mass: 281.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O2
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 440307 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 66.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003834970
ELECTRON MICROSCOPYf_angle_d0.586247682
ELECTRON MICROSCOPYf_chiral_restr0.04115414
ELECTRON MICROSCOPYf_plane_restr0.00436104
ELECTRON MICROSCOPYf_dihedral_angle_d17.173812776

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