[English] 日本語
Yorodumi
- EMDB-27658: cryoEM map of de novo hallucinated homooligomer of C15-C5 symmetr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27658
TitlecryoEM map of de novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
Map dataEM map of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Sample
  • Complex: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
    • Protein or peptide: HALC15-5_262
KeywordsDe novo protein design / Computational protein design / Machine learning / Hallucination / homo-oligomers / DE NOVO PROTEIN
Biological speciesEscherichia coli (E. coli) / Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsWicky BIM / Milles LF / Courbet AC / Baker D
Funding support United States, 3 items
OrganizationGrant numberCountry
Other private United States
Other governmentS10OD032290 United States
Other governmentP30 CA015704-40 United States
Citation
Journal: Science / Year: 2022
Title: Hallucinating symmetric protein assemblies.
Authors: B I M Wicky / L F Milles / A Courbet / R J Ragotte / J Dauparas / E Kinfu / S Tipps / R D Kibler / M Baek / F DiMaio / X Li / L Carter / A Kang / H Nguyen / A K Bera / D Baker /
Abstract: Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination ...Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.
#1: Journal: BioRxiv / Year: 2022
Title: Hallucinating protein assemblies
Authors: Wicky BIM / Milles LF / Courbet A / Baker D
History
DepositionJul 19, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27658.png

Downloads & links

-
Map

FileDownload / File: emd_27658.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.3681349 - 1.9633029
Average (Standard dev.)0.0000817919 (±0.0126535995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_27658_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A of C15/C5 symmetric hallucinated protein...

Fileemd_27658_half_map_1.map
Annotationhalf map A of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B of C15/C5 symmetric hallucinated protein...

Fileemd_27658_half_map_2.map
Annotationhalf map B of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : De novo hallucinated homooligomer of C15-C5 symmetry, design HALC...

EntireName: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
Components
  • Complex: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
    • Protein or peptide: HALC15-5_262

-
Supramolecule #1: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC...

SupramoleculeName: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: HALC15-5_262

MacromoleculeName: HALC15-5_262 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant expressionOrganism: Expression vector pET-mod (others)
SequenceString: DVPLTDPKNL NEFLYALGEG LKGMKNLKKL TLTFPSNPLT IPGDISEGFR ELGEGLKGMK NLEELTVTFN DVPLTDPKN LNEFLYALGE GLKGMKNLKK LTLTFPSNPL TIPGDISEGF RELGEGLKGM KNLEELTVTF N DVPLTDPK NLNEFLYALG EGLKGMKNLK ...String:
DVPLTDPKNL NEFLYALGEG LKGMKNLKKL TLTFPSNPLT IPGDISEGFR ELGEGLKGMK NLEELTVTFN DVPLTDPKN LNEFLYALGE GLKGMKNLKK LTLTFPSNPL TIPGDISEGF RELGEGLKGM KNLEELTVTF N DVPLTDPK NLNEFLYALG EGLKGMKNLK KLTLTFPSNP LTIPGDISEG FRELGEGLKG MKNLEELTVT FN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 8.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
25.0 mMTrisTris
GridModel: C-flat-2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 2.5 µm / Nominal defocus min: 1.0 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 563158
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://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