[English] 日本語
Yorodumi
- SASDG85: Wild-type full-length Liver Receptor Homolog-1/Peroxisome Prolife... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDG85
SampleWild-type full-length Liver Receptor Homolog-1/Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha peptide complex bound to the CYP7A1 promoter oligonucleotide duplex.
  • Liver Receptor Homolog-1 (protein), LRH-1, Homo sapiens
  • Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha (protein), PGC1 alpha, Homo sapiens
  • CYP7A1 Promoter Forward (DNA), Homo sapiens
  • CYP7A1 Promoter Reverse (DNA), Homo sapiens
Function / homology
Function and homology information


primary ovarian follicle growth / positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation ...primary ovarian follicle growth / positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation / Sertoli cell development / positive regulation of T cell anergy / positive regulation of stem cell differentiation / embryonic cleavage / bile acid metabolic process / exocrine pancreas development / negative regulation of chondrocyte differentiation / embryo development ending in birth or egg hatching / cartilage development / homeostatic process / calcineurin-mediated signaling / somatic stem cell population maintenance / positive regulation of viral genome replication / positive regulation of T cell proliferation / neurogenesis / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / cholesterol homeostasis / transcription coregulator binding / SUMOylation of intracellular receptors / phospholipid binding / Nuclear Receptor transcription pathway / positive regulation of T cell activation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor ...Nuclear hormone receptor family 5 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Nuclear receptor subfamily 5 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Corey Seacrist (Vanderbilt University)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Wild-type full-length Liver Receptor Homolog-1/Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha peptide complex bound to the CYP7A1 promoter oligonucleotide duplex.
Specimen concentration: 7.5 mg/ml / Entity id: 1884 / 1885 / 1886 / 1887
BufferName: 20 mM TRIS, 150 mM NaCl, 2% v/v glycerol, 0.5 mM CHAPS, 5 mM DTT
pH: 7.5
Entity #1884Name: LRH-1 / Type: protein / Description: Liver Receptor Homolog-1 / Formula weight: 64.144 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O00482
Sequence: MAHHHHHHVD DDDKMSENLY FQSMSSNSDT GDLQESLKHG LTPIGAGLPD RHGSPIPARG RLVMLPKVET EALGLARSHG EQGQMPENMQ VSQFKMVNYS YDEDLEELCP VCGDKVSGYH YGLLTCESCK GFFKRTVQNN KRYTCIENQN CQIDKTQRKR CPYCRFQKCL ...Sequence:
MAHHHHHHVD DDDKMSENLY FQSMSSNSDT GDLQESLKHG LTPIGAGLPD RHGSPIPARG RLVMLPKVET EALGLARSHG EQGQMPENMQ VSQFKMVNYS YDEDLEELCP VCGDKVSGYH YGLLTCESCK GFFKRTVQNN KRYTCIENQN CQIDKTQRKR CPYCRFQKCL SVGMKLEAVR ADRMRGGRNK FGPMYKRDRA LKQQKKALIR ANGLKLEAMS QVIQAMPSDL TISSAIQNIH SASKGLPLNH AALPPTDYDR SPFVTSPISM TMPPHGSLQG YQTYGHFPSR AIKSEYPDPY TSSPESIMGY SYMDSYQTSS PASIPHLILE LLKCEPDEPQ VQAKIMAYLQ QEQANRSKHE KLSTFGLMCK MADQTLFSIV EWARSSIFFR ELKVDDQMKL LQNCWSELLI LDHIYRQVVH GKEGSIFLVT GQQVDYSIIA SQAGATLNNL MSHAQELVAK LRSLQFDQRE FVCLKFLVLF SLDVKNLENF QLVEGVQEQV NAALLDYTMC NYPQQTEKFG QLLLRLPEIR AISMQAEEYL YYKHLNGDVP YNNLLIEMLH AKRA
Entity #1885Name: PGC1 alpha / Type: protein
Description: Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha
Formula weight: 1.522 / Num. of mol.: 1 / Source: Homo sapiens
Sequence:
EEPSLLKKLL LAPA
Entity #1886Type: DNA / Description: CYP7A1 Promoter Forward / Formula weight: 3.75 / Num. of mol.: 1 / Source: Homo sapiens
Sequence:
GTTCAAGGCC AG
Entity #1887Type: DNA / Description: CYP7A1 Promoter Reverse / Formula weight: 3.701 / Num. of mol.: 1 / Source: Homo sapiens
Sequence:
CTGGCCTTGA AC

-
Experimental information

BeamInstrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS)
City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1127 Å / Dist. spec. to detc.: 2.105 mm
DetectorName: Pilatus3 X 2M / Pixsize x: 172 mm
Scan
Title: Wild-type full-length Liver Receptor Homolog-1/Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha peptide complex bound to the CYP7A1 promoter oligonucleotide duplex.
Measurement date: May 26, 2019 / Cell temperature: 20 °C / Exposure time: 3 sec. / Number of frames: 500 / Unit: 1/A /
MinMax
Q0.0153 0.3704
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 318 /
MinMax
Q0.01561 0.3704
P(R) point1 318
R0 130
Result
Type of curve: sec /
ExperimentalPorod
MW67 kDa-
Volume-76 nm3

P(R)GuinierGuinier errorP(R) error
Forward scattering, I023.72 23.89 0.22 -
Radius of gyration, Rg3.907 nm3.819 nm0.046 0.02

MinMax
D-13
Guinier point1 34

+
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