[English] 日本語
Yorodumi
- EMDB-41364: CryoEM Structure of a Computationally Designed T3 Tetrahedral Nanocage -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41364
TitleCryoEM Structure of a Computationally Designed T3 Tetrahedral Nanocage
Map data
Sample
  • Complex: T3 Tetrahedral Cage
    • Protein or peptide: Computationally designed protein
Keywordsexpandable nanomaterial / de novo / t3 tetrahedral nanocage / computationally designed / nanocage / expandable nanomaterials / DE NOVO PROTEIN
Biological speciesunidentified (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsWeidle C / Borst AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: Blueprinting extendable nanomaterials with standardized protein blocks.
Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / ...Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / Nicolas Coudray / S John Calise / Fatima A Davila-Hernandez / Hannah L Han / Kenneth D Carr / Zhe Li / Ryan McHugh / Gabriella Reggiano / Alex Kang / Banumathi Sankaran / Miles S Dickinson / Brian Coventry / T J Brunette / Yulai Liu / Justas Dauparas / Andrew J Borst / Damian Ekiert / Justin M Kollman / Gira Bhabha / David Baker /
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 owing 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 previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional 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
DepositionJul 26, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41364.png

Downloads & links

-
Map

FileDownload / File: emd_41364.map.gz / Format: CCP4 / Size: 448.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 490 pix.
= 436.1 Å		0.89 Å/pix.
x 490 pix.
= 436.1 Å		0.89 Å/pix.
x 490 pix.
= 436.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.057107855 - 1.9096093
Average (Standard dev.)0.0022740548 (±0.036204733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions490490490
Spacing490490490
CellA=B=C: 436.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_41364_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41364_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T3 Tetrahedral Cage

EntireName: T3 Tetrahedral Cage
Components
  • Complex: T3 Tetrahedral Cage
    • Protein or peptide: Computationally designed protein

-
Supramolecule #1: T3 Tetrahedral Cage

SupramoleculeName: T3 Tetrahedral Cage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Protein complex formed during expression. Purified as whole cage.
Source (natural)Organism: unidentified (others)

-
Macromolecule #1: Computationally designed protein

MacromoleculeName: Computationally designed protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 78.253023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELREIAER AEADMREISE LAEELVEDPV YAVAVRGMAL VGAAGVFALG VGGPPEVLEE ARRRVEEAAR EALRKYEEGA DVSELVAEL IRETSRQIAE IAEATIKATD DPEVLEEISE FAEERSRRLS EYAERHVTNP ILAATVVALA EVLSAVVRAR S YGAPEEVG ...String:
MEELREIAER AEADMREISE LAEELVEDPV YAVAVRGMAL VGAAGVFALG VGGPPEVLEE ARRRVEEAAR EALRKYEEGA DVSELVAEL IRETSRQIAE IAEATIKATD DPEVLEEISE FAEERSRRLS EYAERHVTNP ILAATVVALA EVLSAVVRAR S YGAPEEVG EKAVKEVREA SEEALERYKK GEDVSELVAE LIRETSRQIA EIAEATIKAT DDPEVLEEIS EFAEERSRRL SE YAERHVT NPILAATVVA LAEVLSAVVR ARSYGAPEEV GEKAVKEVRE ASEEALERYK EGADESELVA EVMTATAEAV GEI AEATIE ATDDPEKRRK IAEFAREKMR RIRELARKLV EDPVLAAAVA ARALVLSAAV FAKAYGGPEE YSRLMRRWVE KAAE LARRA RRLGADESVL VAALMRVAAI AVTAIAMMTV MGVQNAPPEE RERILAEATE MIARVLAEAT RRVMKRLEDP EAAAE LALA TIEAITELFV DALEIIRSGE VASRLAKSGI EVIAELAEAA IEHIDDPEQL KKIVKKAAEA IKKIVEELIK KDVEDE LLA EVTSEGNRKL SRITSKALTK IKDEKAAAEL TIEAIEAITE NFLLALERIK DGEVAAKLAE DGLLEIYRLA VSGIEHI DN PEELEKIVKK TEEAVERIVE ALEKKDVEPE LKEEVEELGK KLVEIVRKLA ERKGGSGGSW GHHHHHHG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm

+
Image processing

Particle selectionNumber selected: 1451934
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 266100
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 11 / Avg.num./class: 34398 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: See publication
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: cross-correlation coefficient
Output model

PDB-8tl7:
CryoEM Structure of a Computationally Designed T3 Tetrahedral Nanocage

+
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