[English] 日本語
Yorodumi
- SASDFU9: Adhesion G-protein coupled receptor G6 - zfGpr126 S1 (+ss) ECR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFU9
SampleAdhesion G-protein coupled receptor G6 - zfGpr126 S1 (+ss) ECR
  • Adhesion G-protein coupled receptor G6 S1 (protein), Gpr126, Danio rerio
Function / homology
Function and homology information


myelination of posterior lateral line nerve axons / EGR2 and SOX10-mediated initiation of Schwann cell myelination / semicircular canal fusion / regulation of sprouting angiogenesis / Schwann cell differentiation / peripheral nervous system myelin formation / ear development / myelination in peripheral nervous system / heart trabecula formation / extracellular matrix binding ...myelination of posterior lateral line nerve axons / EGR2 and SOX10-mediated initiation of Schwann cell myelination / semicircular canal fusion / regulation of sprouting angiogenesis / Schwann cell differentiation / peripheral nervous system myelin formation / ear development / myelination in peripheral nervous system / heart trabecula formation / extracellular matrix binding / laminin binding / collagen binding / myelination / mitochondrion organization / cAMP-mediated signaling / ossification / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heart development / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / CUB domain ...Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Adhesion G-protein coupled receptor G6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Contact author
  • Katherine Leon (Uchicago, The University of Chicago, Edward H. Levi Hall 5801 South Ellis Avenue Chicago, Illinois 60637 773.702.1234)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Adhesion G-protein coupled receptor G6 - zfGpr126 S1 (+ss) ECR
Specimen concentration: 2.7 mg/ml
BufferName: 150 mM NaCl, 20 mM HEPES / pH: 7.5
Entity #1777Name: Gpr126 / Type: protein / Description: Adhesion G-protein coupled receptor G6 S1 / Formula weight: 88.708 / Num. of mol.: 1 / Source: Danio rerio / References: UniProt: C6KFA3
Sequence: ASTSCNVVLT DSQGSFTSPC YPNDYPPSQS CNWTIQAPAG FIVQITFLDF ELEEAQGCIY DRVVVKTGTS DAKFCGLTAN GLTLNSTGNV MEVFFNSDFS VQKKGFHISY KQVAVTLRNQ KVTMPKSSKT ILRVSNSISI PVLTAFTVCF EIARTAQKAT ETIFTLSDAA ...Sequence:
ASTSCNVVLT DSQGSFTSPC YPNDYPPSQS CNWTIQAPAG FIVQITFLDF ELEEAQGCIY DRVVVKTGTS DAKFCGLTAN GLTLNSTGNV MEVFFNSDFS VQKKGFHISY KQVAVTLRNQ KVTMPKSSKT ILRVSNSISI PVLTAFTVCF EIARTAQKAT ETIFTLSDAA GTSILAFEKT SNGMELFIGA SYCSVDNFLT SSDITATMKP LCLTWTKSSG LIGVYFEGHY FSSICSASQI YTLQSGGLLQ IAGKGSSSVS VDDQNLDGFI YNFRLWDHAM LSSELSALTC DTVGNVVDWD HSYWTIPGSS TQTDSTLSCS TAITTLSPGT AGCASGLGCP ATLTVTITSI ATTNIIPTNA TTHEDIFYRS TLVVTDEQTP DRDATAIISQ WLNQTFQNWM YRVYVDGISL QLITVLSRIT TTRQIYLALL VYKNTTDVNL AEVEIESMLR SAPAIGNGLT LDSVTVNLME NCQADEFPVH YRWPESRPTV TQYVPCFPYK DRNASRTCMI NRDNYTSFWA LPDRGNCTNI TSITVSQENA MDVAVQLADI SNNGLSKEEL TQVVTKVMEL VNIAKINATL ASTVVTIISN VMVSSEDAQK DASETALKAV DELVQKIEFD GPSLTISSKN LVVGVSALDT TNFNGSTLSA FIATNTTDPQ IDFDSEAHNA LAVVTLPPTL LQNLSLSQIE KVSRINFMFF GRTGLFQDHQ NNGLTLNSYV VASSVGNFTI KNLQDPVRIE IAHLEYQKDP NPQCVFWDFN LQNYSGGWNS DGCKVGSDSN SNRTVCLCNH LTHFGILMDV SRAHHHHHHH H

-
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: 0.103 Å / Dist. spec. to detc.: 1 mm
DetectorName: Pilatus3 X 1M / Pixsize x: 0.172 mm
Scan
Title: Adhesion G-protein coupled receptor G6 - zfGpr126 S1 (+ss) ECR
Measurement date: Jun 28, 2018 / Storage temperature: 4 °C / Cell temperature: 22 °C / Exposure time: 0.8 sec. / Number of frames: 1234 / Unit: 1/A /
MinMax
Q0.0052 0.3816
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 296 /
MinMax
Q0.008714 0.189
P(R) point11 306
R0 148
Result
D max: 14.8 / Type of curve: sec /
ExperimentalPorod
MW107.9 kDa121 kDa
Volume-191 nm3

P(R)GuinierGuinier error
Forward scattering, I090.76 90.2641 0.4052
Radius of gyration, Rg4.34 nm4.247 nm0.027

+
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