[English] 日本語
Yorodumi
- SASDDZ8: Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDDZ8
SampleDesigned hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)
  • Fusion protein of LSm and MyoX-coil (protein), TIP60 protomer, Artificial protein
Biological speciesArtificial protein
CitationDate: 2018 Jul 31
Title: Design of hollow protein nanoparticles with modifiable interior and exterior surfaces
Authors: Kawakami N / Kondo H / Matsuzawa Y / Hayasaka K / Nasu E / Sasahara K / Arai R
Contact author
  • Ryoichi Arai (Shinshu University)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2152
Type: dummy / Radius of dummy atoms: 8.25 A / Chi-square value: 0.012
Search similar-shape structures of this assembly by Omokage search (details)
Model #2153
Type: dummy / Radius of dummy atoms: 8.25 A / Chi-square value: 0.012
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)
Specimen concentration: 0.98-4.97
BufferName: 25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol / pH: 8
Entity #1158Name: TIP60 protomer / Type: protein / Description: Fusion protein of LSm and MyoX-coil / Formula weight: 17.766 / Source: Artificial protein
Sequence:
MGSSHHHHHH SQDPKNIKIM RLVTGEDIIG NISESQGLIT IKKAFVIIPM QATPGKPVQL VLSPWQPYTD DKEIVIDDSK VITITSPKDD IIKSYESHTR VLENKQVEEI LRLEKEIEDL QRMKEQQELS LTEASLQKLQ ERRDQELRRL EEE

-
Experimental information

BeamInstrument name: Photon Factory (PF), High Energy Accelerator Research Organization (KEK) BL-6A
City: Tsukuba / 国: Japan / Type of source: X-ray synchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.023 mm
DetectorName: Pilatus3 1M / Type: Reverse-biased silicon diode array / Pixsize x: 172 mm
Scan
Title: Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)
Measurement date: Nov 11, 2017 / Cell temperature: 25 °C / Exposure time: 5 sec. / Number of frames: 30 / Unit: 1/nm /
MinMax
Q0.057 2.603
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 221 /
MinMax
Q0.0676623 0.85099
P(R) point1 221
R0 23
Result
Type of curve: extrapolated
Comments: The ab initio dummy atom bead models displayed in this entry are: Top - a refined DAMMIN model and corresponding fit generated from 20 individual model spatial alignments; Bottom - the bead- ...Comments: The ab initio dummy atom bead models displayed in this entry are: Top - a refined DAMMIN model and corresponding fit generated from 20 individual model spatial alignments; Bottom - the bead-occupancy and volume-corrected (averaged) spatial representation of TIP60 (DAMFILT) obtained from 20 individual model spatial alignments.
ExperimentalStandard
MW1063 kDa1063 kDa

P(R)GuinierGuinier error
Forward scattering, I00.6241 0.643 0.001
Radius of gyration, Rg8.952 nm9.39 nm0.06

MinMax
D-23
Guinier point4 23

+
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