[English] 日本語
Yorodumi
- SASDDX2: EspG3-PE5/PPE4 complex from M. tuberculosis (EspG3 chaperone from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDDX2
SampleEspG3-PE5/PPE4 complex from M. tuberculosis
  • EspG3 chaperone from Mycobacterium tuberculosis (protein), EspG3Mtb, Mycobacterium tuberculosis
  • PE5 from Mycobacterium tuberculosis (protein), PE5, Mycobacterium tuberculosis
  • PPE4 from Mycobacterium tuberculosis (protein), PPE4, Mycobacterium tuberculosis
Function / homology
Function and homology information


cell envelope / response to host immune response / cell surface / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
PPE-PPW subfamily, C-terminal / PPE-PPW subfamily C-terminal region / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / PPE superfamily / EspG family / EspG family
Similarity search - Domain/homology
PE family immunomodulator PE5 / PPE family protein PPE4 / ESX-3 secretion-associated protein EspG3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
CitationDate: 2018 Jan 25
Title: Structural variability of EspG chaperones from mycobacterial ESX-1, ESX-3 and ESX-5 type VII secretion systems
Authors: Tuukkanen A / Freire D / Chan S / Arbing M / Reed R / Evans T / Zenkeviciutė G / Kim J / Kahng S / Sawaya M / Wilmanns M / Eisenberg D / Parret A
Contact author
  • Anne Tuukkanen (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: EspG3-PE5/PPE4 complex from M. tuberculosis / Specimen concentration: 1.22 mg/ml / Entity id: 927 / 941 / 942
BufferName: 20 mM HEPES pH 7.5, 150 mM NaCl / pH: 7.5
Entity #927Name: EspG3Mtb / Type: protein
Description: EspG3 chaperone from Mycobacterium tuberculosis
Formula weight: 33.6 / Source: Mycobacterium tuberculosis / References: UniProt: P9WJC6
Sequence: MHHHHHHENL YFQGSHMDAT PNAVELTVDN AWFIAETIGA GTFPWVLAIT MPYSDAAQRG AFVDRQRDEL TRMGLLSPQG VINPAVADWI KVVCFPDRWL DLRYVGPASA DGACELLRGI VALRTGTGKT SNKTGNGVVA LRNAQLVTFT AMDIDDPRAL VPILGVGLAH ...Sequence:
MHHHHHHENL YFQGSHMDAT PNAVELTVDN AWFIAETIGA GTFPWVLAIT MPYSDAAQRG AFVDRQRDEL TRMGLLSPQG VINPAVADWI KVVCFPDRWL DLRYVGPASA DGACELLRGI VALRTGTGKT SNKTGNGVVA LRNAQLVTFT AMDIDDPRAL VPILGVGLAH RPPARFDEFS LPTRVGARAD ERLRSGVPLG EVVDYLGIPA SARPVVESVF SGPRSYVEIV AGCNRDGRHT TTEVGLSIVD TSAGRVLVSP SRAFDGEWVS TFSPGTPFAI AVAIQTLTAC LPDGQWFPGQ RVSRDFSTQS S
Entity #941Name: PE5 / Type: protein / Description: PE5 from Mycobacterium tuberculosis / Formula weight: 9.6 / Num. of mol.: 1 / Source: Mycobacterium tuberculosis / References: UniProt: L7N695
Sequence:
MTLRVVPEGL AAASAAVEAL TARLAAAHAS AAPVITAVVP PAADPVSLQT AAGFSAQGVE HAVVTAEGVE ELGRAGVGVG ESGASYLAGD AAAAATYGVV GG
Entity #942Name: PPE4 / Type: protein / Description: PPE4 from Mycobacterium tuberculosis / Formula weight: 51.8 / Num. of mol.: 1 / Source: Mycobacterium tuberculosis / References: UniProt: P9WI43
Sequence: MAAPIWMASP PEVHSALLSN GPGPGSLVAA ATAWSQLSAE YASTAAELSG LLGAVPGWAW QGPSAEWYVA AHLPYVAWLT QASADAAGAA AQHEAAAAAY TTALAAMPTL AELAANHVIH TVLVATNFFG INTIPITLNE ADYVRMWLQA AAVMGLYQAA SGAALASAPR ...Sequence:
MAAPIWMASP PEVHSALLSN GPGPGSLVAA ATAWSQLSAE YASTAAELSG LLGAVPGWAW QGPSAEWYVA AHLPYVAWLT QASADAAGAA AQHEAAAAAY TTALAAMPTL AELAANHVIH TVLVATNFFG INTIPITLNE ADYVRMWLQA AAVMGLYQAA SGAALASAPR TVPAPTVMNP GGGAASTVGA VNPWQWLLAL LQQLWNAYTG FYGWMLQLIW QFLQDPIGNS IKIIIAFLTN PIQALITYGP LLFALGYQIF FNLVGWPTWG MILSSPFLLP AGLGLGLAAI AFLPIVLAPA VIPPASTPLA AAAVAAGSVW PAVSMAVTGA GTAGAATPAA GAAPSAGAAP APAAPATASF AYAVGGSGDW GPSLGPTVGG RGGIKAPAAT VPAAAAAAAT RGQSRARRRR RSELRDYGDE FLDMDSDSGF GPSTGDHGAQ ASERGAGTLG FAGTATKERR VRAVGLTALA GDEFGNGPRM PMVPGTWEQG SNEPEAPDGS GRGGGDGLPH DSK

-
Experimental information

BeamInstrument name: Diamond Light Source B21 / City: Oxfordshire / 国: UK / Shape: 1 x 5 mm / Type of source: X-ray synchrotron
DetectorName: Pilatus 2M
Scan
Title: EspG3-PE5/PPE4 complex from M. tuberculosis / Measurement date: Jun 15, 2015 / Unit: 1/nm /
MinMax
Q0.0834 4.0114
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 698 /
MinMax
Q0.105427 2.02128
P(R) point1 698
R0 14.2
Result
Experimental MW: 83 kDa / Type of curve: single_conc
P(R)GuinierGuinier error
Forward scattering, I00.003034 0.00299 0.00015
Radius of gyration, Rg4.197 nm3.98 nm0.03

MinMax
D-14.2
Guinier point9 90

+
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://pdbjlvh1.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