[English] 日本語
Yorodumi
- EMDB-23168: Dihedral ring D2_Wm-01 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23168
TitleDihedral ring D2_Wm-01
Map data
Sample
  • Complex: D2_Wm-01
    • Protein or peptide: D2_Wm-01A
    • Protein or peptide: D2_Wm-01B
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsPark YJ / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
CitationJournal: Nat Commun / Year: 2021
Title: Design of multi-scale protein complexes by hierarchical building block fusion.
Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una ...Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una Nattermann / Evelyn Tsai / Ayesha Saleem / Cameron M Chow / Damian Ekiert / Gira Bhabha / David Veesler / David Baker /
Abstract: A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two ...A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
History
DepositionDec 21, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.57
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.57
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23168.png

Downloads & links

-
Map

FileDownload / File: emd_23168.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.4 Å/pix.
x 80 pix.
= 512. Å		6.4 Å/pix.
x 80 pix.
= 512. Å		6.4 Å/pix.
x 80 pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.57 / Movie #1: 1.57
Minimum - Maximum-0.74174297 - 8.107711
Average (Standard dev.)-0.0076911286 (±0.32813776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 512.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.46.46.4
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.7428.108-0.008

-
Supplemental data

-
Additional map: #1

Fileemd_23168_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_23168_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_23168_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : D2_Wm-01

EntireName: D2_Wm-01
Components
  • Complex: D2_Wm-01
    • Protein or peptide: D2_Wm-01A
    • Protein or peptide: D2_Wm-01B

-
Supramolecule #1: D2_Wm-01

SupramoleculeName: D2_Wm-01 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: D2_Wm-01A

MacromoleculeName: D2_Wm-01A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MGTREESLKE QLRSLREQAE LAARLLRLLK ELERLQREGS SDEDVRELLR EIKELVAEII KLIM EQLLL IAEQLLGRSE AAELALRAIR LALELCRQST DLEECLRLLK TAIKALENAL RHPDSTTAK ARLMAITARL LAQQLRTQHP DSQAARDAEK LADQAERAVR ...String:
MGTREESLKE QLRSLREQAE LAARLLRLLK ELERLQREGS SDEDVRELLR EIKELVAEII KLIM EQLLL IAEQLLGRSE AAELALRAIR LALELCRQST DLEECLRLLK TAIKALENAL RHPDSTTAK ARLMAITARL LAQQLRTQHP DSQAARDAEK LADQAERAVR LATRLYEEHP NAEISEMCSQ AAYA AALMA SIAAILAQRH PDSQIARDLI RLASELAEMV KRMCERGGSW GLEHHHHHH

-
Macromolecule #2: D2_Wm-01B

MacromoleculeName: D2_Wm-01B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MGTREELAKE LLRSLREQAE SLARQLRLLK ELERLQREGS SDEDVRELLR EIKELAAEQI KLIM EQLLL IAELTLGRSE AAELALDAIR QALEACRTMD NQEACTRLLK LAIQMLELAT RAPDAEAAK LALEAAKKAI ELANRHPGSQ AAEDATKLAQ QAMEAVRLAL ...String:
MGTREELAKE LLRSLREQAE SLARQLRLLK ELERLQREGS SDEDVRELLR EIKELAAEQI KLIM EQLLL IAELTLGRSE AAELALDAIR QALEACRTMD NQEACTRLLK LAIQMLELAT RAPDAEAAK LALEAAKKAI ELANRHPGSQ AAEDATKLAQ QAMEAVRLAL KLYEEHPNAD IADLCRRAAA EAAE AASKA AELAQRHPDS QAARDAIKLA SQAAEAVKLA CELAQEHPNA DKAKLCILLA SAAALLASI AAMLAQRHPD SQEARDMIRI ASELAELVKE ICER

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: UF
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified

-
Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

-
Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16671
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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