[English] 日本語
Yorodumi
- PDB-1yuc: Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yuc
TitleHuman Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP
Components
  • Nuclear receptor 0B2
  • Orphan nuclear receptor NR5A2
KeywordsTRANSCRIPTION REGULATION / Liver Receptor Homologue 1 / Nuclear Receptor Ligand Binding Domain / LRH-1 / Phospholipid / SHP / Small Heterodimer Partner
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / embryo development ending in birth or egg hatching ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / embryo development ending in birth or egg hatching / nuclear thyroid hormone receptor binding / homeostatic process / animal organ regeneration / positive regulation of viral genome replication / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / cholesterol metabolic process / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / cholesterol homeostasis / transcription coregulator binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / phospholipid binding / positive regulation of insulin secretion / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / Nuclear Receptor transcription pathway / circadian rhythm / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EPH / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOrtlund, E.A. / Yoonkwang, L. / Solomon, I.H. / Hager, J.M. / Safi, R. / Choi, Y. / Guan, Z. / Tripathy, A. / Raetz, C.R.H. / McDonnell, D.P. ...Ortlund, E.A. / Yoonkwang, L. / Solomon, I.H. / Hager, J.M. / Safi, R. / Choi, Y. / Guan, Z. / Tripathy, A. / Raetz, C.R.H. / McDonnell, D.P. / Moore, D.D. / Redinbo, M.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP
Authors: Ortlund, E.A. / Lee, Y. / Solomon, I.H. / Hager, J.M. / Safi, R. / Choi, Y. / Guan, Z. / Tripathy, A. / Raetz, C.R.H. / McDonnell, D.P. / Moore, D.D. / Redinbo, M.R.
History
DepositionFeb 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Orphan nuclear receptor NR5A2
B: Orphan nuclear receptor NR5A2
C: Nuclear receptor 0B2
D: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5159
Polymers61,8194
Non-polymers1,6965
Water4,414245
1
A: Orphan nuclear receptor NR5A2
C: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7124
Polymers30,9102
Non-polymers8022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-19 kcal/mol
Surface area12620 Å2
MethodPISA
2
B: Orphan nuclear receptor NR5A2
D: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8045
Polymers30,9102
Non-polymers8943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-16 kcal/mol
Surface area12540 Å2
MethodPISA
3
B: Orphan nuclear receptor NR5A2
D: Nuclear receptor 0B2
hetero molecules

A: Orphan nuclear receptor NR5A2
C: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5159
Polymers61,8194
Non-polymers1,6965
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area7380 Å2
ΔGint-45 kcal/mol
Surface area23520 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-37 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.670, 59.640, 73.240
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

-
Components

#1: Protein Orphan nuclear receptor NR5A2 / Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / ...Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / hB1F / CYP7A promoter binding factor / Liver Receptor Homologue 1


Mass: 29459.893 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2 / Plasmid: PMALCH10T / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor 0B2 / Orphan nuclear receptor SHP / small heterodimer partner


Mass: 1449.673 Da / Num. of mol.: 2 / Fragment: NR Box1 / Source method: obtained synthetically / Details: sequence occurs natuarlly in Homo sapiens / References: UniProt: Q15466
#3: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 709.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2004
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 42718 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.15 / Rsym value: 0.309 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
MOLREPphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 236131.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2082 5 %RANDOM
Rwork0.217 ---
all0.2171 ---
obs0.2171 41458 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6294 Å2 / ksol: 0.348664 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å23.81 Å2
2---1.14 Å20 Å2
3---5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 112 245 4443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 332 5.1 %
Rwork0.233 6166 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMPTY.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GOL.PARION.TOP
X-RAY DIFFRACTION5PTY.PARGOL.PAR

+
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