[English] 日本語
Yorodumi
- SASDDD6: Human Guanylate-binding protein (hGBP1) (Guanylate-binding protein 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDDD6
SampleHuman Guanylate-binding protein (hGBP1)
  • Guanylate-binding protein 1 (protein), Homo sapiens
Function / homology
Function and homology information


GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / cytokine binding / defense response to protozoan / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Andreas Stadler (Forschungszentrum Jülich)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1969
Type: dummy / Software: (2.7.1) / Radius of dummy atoms: 3.25 A / Chi-square value: 2.950
Search similar-shape structures of this assembly by Omokage search (details)
Model #1995
Type: dummy / Software: (2.8.3) / Radius of dummy atoms: 1.50 A / Chi-square value: 2.950
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Human Guanylate-binding protein (hGBP1) / Specimen concentration: 16.1 mg/ml
BufferName: 50 mM TRIS, 5 mM MgCl2, 150 mM NaCl / pH: 7.9
Entity #1063Type: protein / Description: Guanylate-binding protein 1 / Formula weight: 67.629 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P32455
Sequence: MASEIHMTGP MCLIENTNGR LMANPEALKI LSAITQPMVV VAIVGLYRTG KSYLMNKLAG KKKGFSLGST VQSHTKGIWM WCVPHPKKPG HILVLLDTEG LGDVEKGDNQ NDSWIFALAV LLSSTFVYNS IGTINQQAMD QLYYVTELTH RIRSKSSPDE NENEVEDSAD ...Sequence:
MASEIHMTGP MCLIENTNGR LMANPEALKI LSAITQPMVV VAIVGLYRTG KSYLMNKLAG KKKGFSLGST VQSHTKGIWM WCVPHPKKPG HILVLLDTEG LGDVEKGDNQ NDSWIFALAV LLSSTFVYNS IGTINQQAMD QLYYVTELTH RIRSKSSPDE NENEVEDSAD FVSFFPDFVW TLRDFSLDLE ADGQPLTPDE YLTYSLKLKK GTSQKDETFN LPRLCIRKFF PKKKCFVFDR PVHRRKLAQL EKLQDEELDP EFVQQVADFC SYIFSNSKTK TLSGGIQVNG PRLESLVLTY VNAISSGDLP CMENAVLALA QIENSAAVQK AIAHYEQQMG QKVQLPTETL QELLDLHRDS EREAIEVFIR SSFKDVDHLF QKELAAQLEK KRDDFCKQNQ EASSDRCSAL LQVIFSPLEE EVKAGIYSKP GGYRLFVQKL QDLKKKYYEE PRKGIQAEEI LQTYLKSKES MTDAILQTDQ TLTEKEKEIE VERVKAESAQ ASAKMLQEMQ RKNEQMMEQK ERSYQEHLKQ LTEKMENDRV QLLKEQERTL ALKLQEQEQL LKEGFQKESR IMKNEIQDLQ TKMRRRKAC

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.876 mm
DetectorName: Pilatus 1M
Scan
Title: Human Guanylate-binding protein (hGBP1) / Measurement date: Apr 30, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 114 / Unit: 1/nm /
MinMax
Q0.0606 4.9445
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 413 /
MinMax
Q0.173204 2.08788
P(R) point1 413
R0 14.4
Result
Type of curve: sec
Comments: Column type: Size exclusion chromatography (Superdex 200 10/300 GL, GE Healthcare) flow rate: 0.5 ml/min.
ExperimentalPorod
MW65.3 kDa66.1 kDa
Volume-104.9 nm3

P(R)GuinierGuinier error
Forward scattering, I066.1 65.9 0.06
Radius of gyration, Rg4.018 nm3.89 nm0.06

MinMax
D-14.4
Guinier point31 52

+
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