[English] 日本語
Yorodumi
- SASDGC7: Plasmodium falciparum Membrane Occupation and Recognition Nexus (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDGC7
SamplePlasmodium falciparum Membrane Occupation and Recognition Nexus (MORN1) repeats 7-15
  • MORN repeat-containing protein 1 (protein), pf MORN1 delta 6, Plasmodium falciparum (isolate 3D7)
Function / homologyPossible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / MORN repeat-containing protein 1
Function and homology information
Biological speciesPlasmodium falciparum (isolate 3D7) (eukaryote)
Contact author
  • Melissa Graewert (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3818
Type: dummy / Software: (SUPCOMB 23 (r9988)) / Radius of dummy atoms: 4.00 A / Chi-square value: 1.126 / P-value: 0.082356
Model #3819
Type: atomic / Chi-square value: 1.372

-
Sample

SampleName: Plasmodium falciparum Membrane Occupation and Recognition Nexus (MORN1) repeats 7-15
Specimen concentration: 1 mg/ml
BufferName: 20 mM Tris-HCl, 100 mM NaCl / pH: 7.5
Entity #1925Name: pf MORN1 delta 6 / Type: protein / Description: MORN repeat-containing protein 1 / Formula weight: 23.074 / Num. of mol.: 2 / Source: Plasmodium falciparum (isolate 3D7) / References: UniProt: Q8IJ93
Sequence: GRGTYFFADG GIYEGDWVDG KMEGKGVYKY LNGNKYEGEW INDMKNGYGT LAYVNGELYE GYWKNDKVHG KGTLTYSKGD KYIGEWKYAK KCGEGELIYA SGDKFKGQWK NDKANGYGIL LYNNGNKYEG EWLDDHRHGM GTFTCKEDGT IYSGHFQFNR KHGKGTLTFV ...Sequence:
GRGTYFFADG GIYEGDWVDG KMEGKGVYKY LNGNKYEGEW INDMKNGYGT LAYVNGELYE GYWKNDKVHG KGTLTYSKGD KYIGEWKYAK KCGEGELIYA SGDKFKGQWK NDKANGYGIL LYNNGNKYEG EWLDDHRHGM GTFTCKEDGT IYSGHFQFNR KHGKGTLTFV NGHILQGIWN SGLLEKVINY ELTPSSPWND PDL

-
Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 2M
Scan
Title: Plasmodium falciparum Membrane Occupation and Recognition Nexus (MORN1) repeats 7-15
Measurement date: Dec 2, 2017 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
MinMax
Q0.0891 3.3396
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 714 /
MinMax
Q0.119507 2.09193
P(R) point1 714
R0 16
Result
Type of curve: single_conc /
ExperimentalStandardPorod
MW32 kDa52 kDa33 kDa
Volume--52 nm3

P(R)GuinierGuinier error
Forward scattering, I00.05974 0.058 0.00032
Radius of gyration, Rg4.173 nm3.82 nm0.13

MinMax
D-16
Guinier point12 91

+
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