[English] 日本語
Yorodumi
- EMDB-29915: CryoEM map of a de novo designed octahedral nanocage with program... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29915
TitleCryoEM map of a de novo designed octahedral nanocage with programmable volume; design cage_O4_34
Map dataDeepEMhancer sharpened map
Sample
  • Complex: cage_O4_34
    • Protein or peptide: cage_O4_34
Keywordsoctahedral nanocage / octahedra / nanocage / nanomaterial / computational design / de novo / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.52 Å
AuthorsKibler RD / Borst AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2023
Title: Blueprinting expandable nanomaterials with standardized protein building blocks.
Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures . Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints.
History
DepositionFeb 24, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29915.png

Downloads & links

-
Map

FileDownload / File: emd_29915.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Voxel sizeX=Y=Z: 1.248 Å
Density
Contour LevelBy AUTHOR: 0.153
Minimum - Maximum-0.00093979423 - 1.5882615
Average (Standard dev.)0.005034749 (±0.049945626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 474.24002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_29915_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_29915_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_29915_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : cage_O4_34

EntireName: cage_O4_34
Components
  • Complex: cage_O4_34
    • Protein or peptide: cage_O4_34

-
Supramolecule #1: cage_O4_34

SupramoleculeName: cage_O4_34 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The smallest size of a de novo designed octahedral nanocage with programmable volume
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: cage_O4_34

MacromoleculeName: cage_O4_34 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEEKREIAEF AREMMEEISE RVERYVEDPV LATAVRGRAI VESAAVFAKT IGGDIEKLDE AREEVERAAE EALRRREEGA DVSELVAELI RETSRQIAEI AEATIKATDD PEVLEEISEF AEERSRRLSE YAERHVTNPI LAATVVALAE VLSAVVRARS YGAPEEVGEK ...String:
MEEKREIAEF AREMMEEISE RVERYVEDPV LATAVRGRAI VESAAVFAKT IGGDIEKLDE AREEVERAAE EALRRREEGA DVSELVAELI RETSRQIAEI AEATIKATDD PEVLEEISEF AEERSRRLSE YAERHVTNPI LAATVVALAE VLSAVVRARS YGAPEEVGEK AVKEVREASE EALERYKEGA DESELIAEIM EATAEAVGKI AEAAIEATDD PEKRRRIARW AREQMRRLSR RAEELVEDPV LAMTVFARAQ ILAAAVFGKA VGMPEIVSEH ARRMVRLAGE AALALKKEGA DVSRLVAMVG RVTSIAVGMI AKATVSDSPV EITKELIRAF KEITEELIKA GVDGKHLNEA VRLGSEAVNE LVEEAVKEGT PVEEVTESAI KGLEAVTEMA IEAMKAGGDP LEMARIVAEL AEKAIDVVAK MGAPGTYMLA MIMAASVAHR RIVEAAIKAG APGEVLEEAV RLAGRVQVRG VEKAAELGTP KTLVEAAGEL GLATVRRMAE LAIEAGGDRE RMEEIIREVE EAMERVIERI EGGSGGSWGH HHHHHG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8 / Details: 25mM Tris, 300mM NaCl
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 42.6 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 17.0 µm / Nominal defocus min: 8.0 µm

+
Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59904
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://pdbjlvh1.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