[English] 日本語
Yorodumi
- EMDB-46767: azoRhuA-bCDRhuA co-assembled nanotubes, 10-start -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46767
TitleazoRhuA-bCDRhuA co-assembled nanotubes, 10-start
Map dataazoRhuA-bCDRhuA co-assembled nanotubes, 10-start
Sample
  • Complex: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA
    • Protein or peptide: L-rhamnulose-1-phosphate aldolase
KeywordsAssembly / LYASE
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 7.8 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
DepositionAug 27, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46767.png

Downloads & links

-
Map

FileDownload / File: emd_46767.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationazoRhuA-bCDRhuA co-assembled nanotubes, 10-start
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 480 pix.
= 825.6 Å		1.72 Å/pix.
x 480 pix.
= 825.6 Å		1.72 Å/pix.
x 480 pix.
= 825.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.84
Minimum - Maximum-0.7463125 - 2.1844134
Average (Standard dev.)0.03797787 (±0.18036239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 825.60004 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: azoRhuA-bCDRhuA co-assembled nanotubes, 10-start, half map B

Fileemd_46767_half_map_1.map
AnnotationazoRhuA-bCDRhuA co-assembled nanotubes, 10-start, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: azoRhuA-bCDRhuA co-assembled nanotubes, 10-start, half map A

Fileemd_46767_half_map_2.map
AnnotationazoRhuA-bCDRhuA co-assembled nanotubes, 10-start, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: L-rhamnulose-1-phosphate aldolase

-
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: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: L-rhamnulose-1-phosphate aldolase

MacromoleculeName: L-rhamnulose-1-phosphate aldolase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSCGA GYHILWGLTN EAVPTSELPA HFLSHSERIK ATNGKDRVIM HCHATNLIAL TYVLENDTAV FTRQLWEGST ...String:
MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSCGA GYHILWGLTN EAVPTSELPA HFLSHSERIK ATNGKDRVIM HCHATNLIAL TYVLENDTAV FTRQLWEGST ECLVVFPDGV GILPWMVPGT DAIGQATAQE MQKHSLVLWP FHGVFGSGPT LDETFGLIDT AEKSAQVLVK VYSMGGMKQT ISREELIALG KRFGVTPLAS ALAL

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -106.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 55635
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1gt7

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more