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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: Zhang Z / Chiang HT / Xia Y / Avakyan N / Sonani RR / Wang F / Egelman EH / De Yoreo JJ / Pozzo LD / Tezcan FA
History
DepositionSep 2, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EMready processed volume map

Fileemd_46826_additional_2.map
AnnotationEMready processed volume map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46826_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46826_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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