[English] 日本語
Yorodumi
- SASDF42: Human serum albumin in complex with somapacitan (Human serum albu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDF42
SampleHuman serum albumin in complex with somapacitan
  • Human serum albumin (protein), HSA, Homo sapiens
  • somapacitan (protein), Homo sapiens
Function / homology
Function and homology information


growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / positive regulation of growth / animal organ development / cell surface receptor signaling pathway via STAT / exogenous protein binding / positive regulation of multicellular organism growth / Ciprofloxacin ADME ...growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / positive regulation of growth / animal organ development / cell surface receptor signaling pathway via STAT / exogenous protein binding / positive regulation of multicellular organism growth / Ciprofloxacin ADME / cellular response to calcium ion starvation / positive regulation of D-glucose transmembrane transport / enterobactin binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / growth hormone receptor signaling pathway / Heme degradation / Aspirin ADME / Prolactin receptor signaling / antioxidant activity / cell surface receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / toxic substance binding / growth hormone receptor signaling pathway via JAK-STAT / Scavenging of heme from plasma / Growth hormone receptor signaling / Recycling of bile acids and salts / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to starvation / response to nutrient levels / platelet alpha granule lumen / cytokine activity / endosome lumen / fatty acid binding / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of MAP kinase activity / growth factor activity / Cytoprotection by HMOX1 / hormone activity / cytokine-mediated signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / response to estradiol / protein-folding chaperone binding / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site ...Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Four-helical cytokine-like, core
Similarity search - Domain/homology
Somatotropin / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Eva Johansson (Novo Nordisk A/S)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2804
Type: atomic / Chi-square value: 2.1025 / P-value: 0.002492

-
Sample

SampleName: Human serum albumin in complex with somapacitan / Specimen concentration: 6.3 mg/ml / Entity id: 1469 / 1470
BufferName: 100 mM MES, 140 mM NaCl / pH: 6.5
Entity #1469Name: HSA / Type: protein / Description: Human serum albumin / Formula weight: 66.472 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P02768
Sequence: DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMADC CAKQEPERNE CFLQHKDDNP NLPRLVRPEV DVMCTAFHDN EETFLKKYLY EIARRHPYFY APELLFFAKR YKAAFTECCQ ...Sequence:
DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMADC CAKQEPERNE CFLQHKDDNP NLPRLVRPEV DVMCTAFHDN EETFLKKYLY EIARRHPYFY APELLFFAKR YKAAFTECCQ AADKAACLLP KLDELRDEGK ASSAKQRLKC ASLQKFGERA FKAWAVARLS QRFPKAEFAE VSKLVTDLTK VHTECCHGDL LECADDRADL AKYICENQDS ISSKLKECCE KPLLEKSHCI AEVENDEMPA DLPSLAADFV ESKDVCKNYA EAKDVFLGMF LYEYARRHPD YSVVLLLRLA KTYETTLEKC CAAADPHECY AKVFDEFKPL VEEPQNLIKQ NCELFEQLGE YKFQNALLVR YTKKVPQVST PTLVEVSRNL GKVGSKCCKH PEAKRMPCAE DYLSVVLNQL CVLHEKTPVS DRVTKCCTES LVNRRPCFSA LEVDETYVPK EFNAETFTFH ADICTLSEKE RQIKKQTALV ELVKHKPKAT KEQLKAVMDD FAAFVEKCCK ADDKETCFAE EGKKLVAASQ AALGL
Entity #1470Type: protein / Description: somapacitan / Formula weight: 22.119 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: P01241
Sequence:
FPTIPLSRLF DNAMLRAHRL HQLAFDTYQE FEEAYIPKEQ KYSFLQNPQT SLCFSESIPT PSNREETQQK SNLELLRISL LLIQSWLEPV QFLRSVFANS CVYGASDSNV YDLLKDLEEG IQTLMGRLED GSPRTGQIFK QTYSKFDTNS HNDDALLKNY GLLYCFRKDM DKVETFLRIV QCRSVEGSCG F

-
Experimental information

BeamInstrument name: Novo Nordisk A/S Rigaku BioSAXS-2000 / City: Maaloev / 国: Denmark / Type of source: X-ray in house / Wavelength: 0.1542 Å
DetectorName: Pilatus 100K / Pixsize x: 172 mm
Scan
Title: Human serum albumin in complex with somapacitan / Measurement date: Sep 4, 2015 / Cell temperature: 25 °C / Exposure time: 3600 sec. / Number of frames: 6 / Unit: 1/A /
MinMax
Q0.0037 0.645
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 127 /
MinMax
Q0.01525 0.1968
P(R) point6 132
R0 139.2
Result
Type of curve: single_conc /
ExperimentalPorod
MW113 kDa126 kDa
Volume-202 nm3

P(R)GuinierGuinier error
Forward scattering, I06.834 6.843 0.02
Radius of gyration, Rg4.12 nm4.06 nm0.02

MinMax
D-13.92
Guinier point6 20

+
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