[English] 日本語
Yorodumi
- SASDG84: Autoinhibited dimer of truncated 6xHis Cytohesin-2 (ARNO, amino a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDG84
SampleAutoinhibited dimer of truncated 6xHis Cytohesin-2 (ARNO, amino acids 2-400) with Inositol 1,3,4,5-tetrakis phosphate (DAMMIF, GASBOR and antiparallel CORAL models)
  • Cytohesin-2 (protein), Cyth2, ARNO, Mus musculus
Function / homology
Function and homology information


extrinsic component of postsynaptic specialization membrane / Intra-Golgi traffic / negative regulation of dendrite development / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / ruffle / guanyl-nucleotide exchange factor activity / adherens junction ...extrinsic component of postsynaptic specialization membrane / Intra-Golgi traffic / negative regulation of dendrite development / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / ruffle / guanyl-nucleotide exchange factor activity / adherens junction / growth cone / postsynapse / lipid binding / glutamatergic synapse / plasma membrane / cytoplasm
Similarity search - Function
Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Contact author
  • David Lambright (UMASS, UMASS Medical School, Worcester, MA, USA)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3648
Type: dummy / Software: (dammif (r9988)) / Radius of dummy atoms: 3.00 A / Symmetry: P1 / Comment: Most representative of 100 DAMMIF models / Chi-square value: 1.219 / P-value: 0.127961
Search similar-shape structures of this assembly by Omokage search (details)
Model #3649
Type: dummy / Software: (DAMFILT 5.0 (r9988)) / Radius of dummy atoms: 4.25 A / Symmetry: P1
Comment: Filtered average of 10 filtered averages of 10 DAMMIF models
Chi-square value: 1.219 / P-value: 0.127961
Search similar-shape structures of this assembly by Omokage search (details)
Model #3682
Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Comment: Most representative of 100 GASBOR models / Chi-square value: 1.30 / P-value: 0.001891
Search similar-shape structures of this assembly by Omokage search (details)
Model #3683
Type: dummy / Software: (DAMFILT 5.0 (r9988)) / Radius of dummy atoms: 3.75 A / Symmetry: P1
Comment: Filtered average of 10 filtered averages of 10 GASBOR models
Chi-square value: 1.30 / P-value: 0.001891
Search similar-shape structures of this assembly by Omokage search (details)
Model #3684
Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P1
Comment: Derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil
Chi-square value: 1.29 / P-value: 0.003841
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Autoinhibited dimer of truncated 6xHis Cytohesin-2 (ARNO, amino acids 2-400) with Inositol 1,3,4,5-tetrakis phosphate (DAMMIF, GASBOR and antiparallel CORAL models)
Specimen concentration: 10 mg/ml
BufferName: 20 mM Tris, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, 0.001 mM insitol 1,3,4,5-tetrakis phosphate
pH: 8
Entity #1857Name: Cyth2, ARNO / Type: protein / Description: Cytohesin-2 / Formula weight: 47.595 / Num. of mol.: 2 / Source: Mus musculus / References: UniProt: P63034
Sequence: MGHHHHHHGS EDGVYEPPDL TPEERMELEN IRRRKQELLV EIQRLREELS EAMSEVEGLE ANEGSKTLQR NRKMAMGRKK FNMDPKKGIQ FLVEHELLQN TPEEIARFLY KGEGLNKTAI GDYLGEREEL NLSVLHAFVD LHEFTDLNLV QALRQFLWSF RLPGEAQKID ...Sequence:
MGHHHHHHGS EDGVYEPPDL TPEERMELEN IRRRKQELLV EIQRLREELS EAMSEVEGLE ANEGSKTLQR NRKMAMGRKK FNMDPKKGIQ FLVEHELLQN TPEEIARFLY KGEGLNKTAI GDYLGEREEL NLSVLHAFVD LHEFTDLNLV QALRQFLWSF RLPGEAQKID RMMEAFAQRY CLCNPGVFQS TDTCYVLSFA VIMLNTSLHN PNVRDKPGLE RFVAMNRGIN EGGDLPEDLL RNLYDSIRNE PFKIPEDDGN DLTHTFFNPD REGWLLKLGG GRVKTWKRRW FILTDNCLYY FEYTTDKEPR GIIPLENLSI REVDDPRKPN CFELYIPNNK GQLIKACKTE ADGRVVEGNH MVYRISAPTQ EEKDEWIKSI QAAVSVDPFY EMLAARKKRI SVKKKQEQP

-
Experimental information

BeamInstrument name: Advanced Photon Source (APS), Argonne National Laboratory BioCAT 18ID
City: Lemont, IL / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å / Dist. spec. to detc.: 2.5 mm
DetectorName: MAR 165 CCD
Scan
Title: Autoinhibited dimer of truncated 6xHis Cytohesin-2 (ARNO, amino acids 2-400) with Inositol 1,3,4,5-tetrakis phosphate (DAMMIF, GASBOR and antiparallel CORAL models)
Measurement date: Nov 15, 2013 / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 121 / Unit: 1/A /
MinMax
Q0.0069 0.3162
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 76 /
MinMax
Q0.00688375 0.316224
P(R) point1 76
R0 270
Result
Type of curve: sec
Comments: The protein was equilibrated with a 1.2 molar excess of inositol 1,3,4,5-tetrakis phosphate (IP4) and concentrated to 10 mg/ml prior to injection.
ExperimentalPorod
MW95 kDa-
Volume-180 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I01.037 0.004 1.03 0.002
Radius of gyration, Rg5.6 nm0.13 5.3 nm0.04

MinMaxError
D-27 0.1
Guinier point1 19 -

+
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