[English] 日本語
Yorodumi
- EMDB-59316: T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-59316
TitleT33-Fus-1A asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Map dataFocused map sharpened
Sample
  • Complex: T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
    • Protein or peptide: T33-Fus-1A-subunit
Keywordsprotein cage / tetrahedral / protein design / nanohedra / nanoparticle / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSan Segundo-Acosta P / LeCoq J / Boskovic J / Aglietti RA / Bowers P / Yeates TO / Castells-Graells R
Funding support Spain, European Union, 3 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2024-161096NA-I00 Spain
European Union (EU)C005/24-ED CV1European Union
Generalitat de CatalunyaIU16-014045 Spain
CitationJournal: To Be Published
Title: Design and structure of protein cages based on helical fusion and machine learning
Authors: San Segundo-Acosta P / LeCoq J / Boskovic J / Aglietti RA / Bowers P / Yeates TO / Castells-Graells R
History
DepositionAug 4, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_59316.png

Downloads & links

-
Map

FileDownload / File: emd_59316.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 416 pix.
= 386.88 Å		0.93 Å/pix.
x 416 pix.
= 386.88 Å		0.93 Å/pix.
x 416 pix.
= 386.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.42544562 - 0.7189125
Average (Standard dev.)0.00008647584 (±0.007616332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 386.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Focused map unsharpened

Fileemd_59316_additional_1.map
AnnotationFocused map unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Consensus map sharpened

Fileemd_59316_additional_2.map
AnnotationConsensus map sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Consensus map unsharpened

Fileemd_59316_additional_3.map
AnnotationConsensus map unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focused half map A

Fileemd_59316_half_map_1.map
AnnotationFocused half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focused half map B

Fileemd_59316_half_map_2.map
AnnotationFocused half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage ba...

EntireName: T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
Components
  • Complex: T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
    • Protein or peptide: T33-Fus-1A-subunit

-
Supramolecule #1: T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage ba...

SupramoleculeName: T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: De novo design protein
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 630 KDa

-
Macromolecule #1: T33-Fus-1A-subunit

MacromoleculeName: T33-Fus-1A-subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.877715 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDPQDLYTWE PKGLAVVDMA LAQESAGLVM LYHFDGYIDA GETGDQIVDQ VLDSLPHQVV ARFDHDRLVD YRARRPLLTF KRDTWSDYE EPTIEVRLVQ DATGAPFLFL SGPEPDVEWE RFAAAVGQIV ERLGVRLSVS FHGIPMGVPH TRPVGITPHG S RTDLVPGH ...String:
MDPQDLYTWE PKGLAVVDMA LAQESAGLVM LYHFDGYIDA GETGDQIVDQ VLDSLPHQVV ARFDHDRLVD YRARRPLLTF KRDTWSDYE EPTIEVRLVQ DATGAPFLFL SGPEPDVEWE RFAAAVGQIV ERLGVRLSVS FHGIPMGVPH TRPVGITPHG S RTDLVPGH RSPFEEAQVP GSAEALVEYR LAQAGHDVLG VAAHVPHYVA RSAYPDAALT VLEAITAATG LVLPGIAHSL RT DAHRTQT EIDRQIQEGD EELIALVRGL ERRADGERID AQLKALKVIP VIAIDNAEDI IPLGKVLAEN GLPAAEITFR SDA AVEAIR LLRQAQPEML IGAGTILNGE QALAAKEAGA TFVVSPGFNP NTVRACDEIG IPIVPGVNNP STVEAALEMG ITTL KFFPA EASGGISMVK SLVGPYGDIR LMPTGGITPS NIDNYLAIPQ VLACGGTWMV DKKLVTNGEW DEIARLTREI VEQVN PGHH HHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8 / Details: 30 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 45sec, 15mA, 0.1bar
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blotting 3 seconds, blot force 0.

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v5.0.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial model generated de novo by ab-initio reconstruction in CryoSPARC from the experimental particle set
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v5.0.4) / Details: The particles were symmetry expanded in T / Number images used: 435000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v5.0.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v5.0.4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v5.0.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: The initial model consisted of a de novo design protein
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-33au:
T33-Fus-1A asymmetric unit - Designed tetrahedral protein cage based on helical fusion and machine learning

+
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