[English] 日本語
Yorodumi
- SASDC27: Saposin nanoparticle (SapNP) SapA:DOPC (saposin-a, sapA + 1,2-dio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDC27
SampleSaposin nanoparticle (SapNP) SapA:DOPC
  • saposin-a (protein), sapA, Homo sapiens
  • 1,2-dioleoyl-sn-glycero-3-phosphocholine (other), DOPC, Synthetic compound
Function / homology
Function and homology information


positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / Glycosphingolipid catabolism ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / Glycosphingolipid catabolism / epithelial cell differentiation involved in prostate gland development / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / enzyme activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / lysosomal lumen / Peptide ligand-binding receptors / regulation of autophagy / phospholipid binding / late endosome / Platelet degranulation / G alpha (i) signalling events / scaffold protein binding / collagen-containing extracellular matrix / protease binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Saposin, chordata / Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 ...Saposin, chordata / Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Synthetic compound (others)
CitationDate: 2018 Feb
Title: Saposin Lipid Nanoparticles: A Highly Versatile and Modular Tool for Membrane Protein Research
Authors: Flayhan A / Mertens H / Ural-Blimke Y / Martinez Molledo M / Svergun D
Contact author
  • Haydyn Mertens (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 #1500
Type: dummy / Software: (2.9.0) / Radius of dummy atoms: 2.10 A / Symmetry: P1 / Chi-square value: 1.214
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Saposin nanoparticle (SapNP) SapA:DOPC / Entity id: 779 / 783
BufferName: PBS / PK: 7 / pH: 7.4
Entity #779Name: sapA / Type: protein / Description: saposin-a / Formula weight: 9.084 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P07602
Sequence:
SMSLPCDICK DVVTAAGDML KDNATEEEIL VYLEKTCDWL PKPNMSASCK EIVDSYLPVI LDIIKGEMSR PGEVCSALNL CES
Entity #783Name: DOPC / Type: other / Description: 1,2-dioleoyl-sn-glycero-3-phosphocholine / Formula weight: 0.78 / Source: Synthetic compound

-
Experimental information

BeamInstrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
DetectorName: Pilatus 2M
Scan
Title: sapAdopc / Measurement date: Dec 15, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
MinMax
Q0.0195 5.0075
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1169 /
MinMax
Q0.104419 3.30551
P(R) point1 1169
R0 11.5
Result
Type of curve: extrapolated
ExperimentalExperimental errorPorodPorod error
MW33 kDa5 56 kDa6
Volume--96 nm310

P(R)P(R) errorGuinierGuinier error
Forward scattering, I039720 40 40271 55
Radius of gyration, Rg4 nm0.1 4.1 nm0.1

MinMaxError
D-11.5 0.5
Guinier point32 105 -

+
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