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- EMDB-46826: Focused region on azoRhuA-bCDRhuA co-assembled nanotubes -

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Basic information

Entry
Database: EMDB / ID: EMD-46826
TitleFocused region on azoRhuA-bCDRhuA co-assembled nanotubes
Map data
Sample
  • Complex: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
    • Protein or peptide: Rhamnulose-1-phosphate aldolase
  • Ligand: ZINC ION
  • Ligand: 1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione
KeywordsAssembly / LYASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhang Z / Sonani RR / Wang F / Egelman EH / Tezcan FA
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46826.png

Downloads & links

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Map

FileDownload / File: emd_46826.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3709447 - 2.2194786
Average (Standard dev.)0.008683947 (±0.072585665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local filtered volume map

Fileemd_46826_additional_1.map
Annotationlocal filtered volume map
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Additional map: EMready processed volume map

Fileemd_46826_additional_2.map
AnnotationEMready processed volume map
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Half map: #1

Fileemd_46826_half_map_1.map
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Half map: #2

Fileemd_46826_half_map_2.map
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Sample components

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Entire : Helical assembly of azobenzene and beta-cyclodextrin modified RhuA

EntireName: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
Components
  • Complex: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
    • Protein or peptide: Rhamnulose-1-phosphate aldolase
  • Ligand: ZINC ION
  • Ligand: 1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione

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Supramolecule #1: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA

SupramoleculeName: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Rhamnulose-1-phosphate aldolase

MacromoleculeName: Rhamnulose-1-phosphate aldolase / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO / EC number: rhamnulose-1-phosphate aldolase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.088361 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAAN LGIVKVDSCG AGYHILWGLT NEAVPTSELP AHFLSHSERI KATNGKDRVI MHCHATNLIA LTYVLENDTA V FTRQLWEG ...String:
MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAAN LGIVKVDSCG AGYHILWGLT NEAVPTSELP AHFLSHSERI KATNGKDRVI MHCHATNLIA LTYVLENDTA V FTRQLWEG STECLVVFPD GVGILPWMVP GTDAIGQATA QEMQKHSLVL WPFHGVFGSG PTLDETFGLI DTAEKSAQVL VK VYSMGGM KQTISREELI ALGKRFGVTP LASALAL

UniProtKB: Rhamnulose-1-phosphate aldolase

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: 1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione

MacromoleculeName: 1-[4-(2-phenylhydrazin-1-yl)phenyl]pyrrolidine-2,5-dione
type: ligand / ID: 4 / Number of copies: 2 / Formula: A1A4G
Molecular weightTheoretical: 281.309 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1gt7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 440307
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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