- PDB-2lpz: Atomic model of the Type-III Secretion System Needle -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2lpz
Title
Atomic model of the Type-III Secretion System Needle
Components
Protein prgI
Keywords
TRANSPORT PROTEIN / type three secretion system / filament / needle / helical assembly
Function / homology
Function and homology information
type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding Similarity search - Function
Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein Similarity search - Domain/homology
A: Protein prgI B: Protein prgI C: Protein prgI D: Protein prgI E: Protein prgI F: Protein prgI G: Protein prgI H: Protein prgI I: Protein prgI J: Protein prgI K: Protein prgI L: Protein prgI M: Protein prgI N: Protein prgI O: Protein prgI P: Protein prgI Q: Protein prgI R: Protein prgI S: Protein prgI T: Protein prgI U: Protein prgI V: Protein prgI W: Protein prgI X: Protein prgI Y: Protein prgI Z: Protein prgI a: Protein prgI b: Protein prgI c: Protein prgI
Method: Monte Carlo, gradient-based optimization / Software ordinal: 3 Details: Monte-Carlo and gradient-based refinement in torsion angle space of the rigid body, backbone and sidechain degrees of freedom
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 1000000 / Conformers submitted total number: 10
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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