[English] 日本語
Yorodumi
- PDB-7jye: Human Liver Receptor Homolog-1 in Complex with 9ChoP and a Fragme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jye
TitleHuman Liver Receptor Homolog-1 in Complex with 9ChoP and a Fragment of Tif2
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / agonist / nuclear receptor
Function / homology
Function and homology information


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 / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation ...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 / primary ovarian follicle growth / 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 / embryo development ending in birth or egg hatching / exocrine pancreas development / cartilage development / negative regulation of chondrocyte differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / calcineurin-mediated signaling / locomotor rhythm / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / somatic stem cell population maintenance / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of viral genome replication / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / hormone-mediated signaling pathway / positive regulation of adipose tissue development / : / neurogenesis / Regulation of lipid metabolism by PPARalpha / positive regulation of T cell proliferation / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cholesterol homeostasis / cellular response to leukemia inhibitory factor / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / phospholipid binding / positive regulation of T cell activation / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / sequence-specific double-stranded DNA binding / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 ...Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
Chem-VQY / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsD'Agostino, E.H. / Mays, S.G. / Ortlund, E.A.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1444932 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008602 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F31DK111171 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008367-27 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK095750 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK114213 United States
United States Department of Agriculture (USDA)3092-5-001-057 United States
CitationJournal: To Be Published
Title: Tapping into a phospholipid-LRH-1 axis yields a powerful anti-inflammatory agent with in vivo activity against colitis
Authors: D'Agostino, E.H. / Mays, S.G. / Flynn, A.F. / Huang, X. / Wang, G. / Liu, X. / Millings, E.J. / Okafor, C.D. / Patel, A. / Cato, M.L. / Cornelison, J.C. / Houtman, R. / Moore, D.D. / ...Authors: D'Agostino, E.H. / Mays, S.G. / Flynn, A.F. / Huang, X. / Wang, G. / Liu, X. / Millings, E.J. / Okafor, C.D. / Patel, A. / Cato, M.L. / Cornelison, J.C. / Houtman, R. / Moore, D.D. / Calvert, J.W. / Jui, N.T. / Ortlund, E.A.
History
DepositionAug 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4913
Polymers29,8812
Non-polymers6111
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization binding assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 89.240, 106.537
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 28401.771 Da / Num. of mol.: 1 / Fragment: nuclear receptor ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1478.756 Da / Num. of mol.: 1 / Fragment: residues 740-751 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-VQY / 9-[(3~{a}~{R},6~{R},6~{a}~{R})-6-oxidanyl-3-phenyl-3~{a}-(1-phenylethenyl)-4,5,6,6~{a}-tetrahydro-1~{H}-pentalen-2-yl]nonyl 2-(trimethyl-$l^{4}-azanyl)ethyl hydrogen phosphate


Mass: 610.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H53NO5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 9-19% tert-butanol, 0-6 % glycerol, 0.1 M tri-sodium citrate pH 4.6

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.48
ReflectionResolution: 2.55→50 Å / Num. obs: 16458 / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.074 / Rrim(I) all: 0.276 / Χ2: 1.049 / Net I/σ(I): 3.6 / Num. measured all: 226693
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.6413.81.95516130.5710.5422.030.405100
2.64-2.7512.51.50816230.6610.441.5730.452100
2.75-2.8714.41.13116200.770.3071.1730.492100
2.87-3.0215.20.91716210.8840.2420.9490.519100
3.02-3.2114.90.63216240.8990.1680.6540.7100
3.21-3.4614.40.45916390.9350.1250.4760.937100
3.46-3.8111.80.30616390.9580.0920.321.499.9
3.81-4.3612.80.19116480.9780.0550.1981.61399.9
4.36-5.4914.90.15916660.9880.0430.1651.75100
5.49-5013.10.17117650.9870.0480.1782.24699.8

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12-2829-000refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JYD

7jyd


Resolution: 2.551→35.512 Å / Cross valid method: THROUGHOUT / σ(F): 105.3 / Phase error: 20.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1871 818 4.98 %
Rwork0.1592 15594 -
obs0.1776 16427 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.73 Å2 / Biso mean: 64.2171 Å2 / Biso min: 26.11 Å2
Refinement stepCycle: final / Resolution: 2.551→35.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 95 18 2166
Biso mean--75.77 49.7 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012144
X-RAY DIFFRACTIONf_angle_d0.322897
X-RAY DIFFRACTIONf_dihedral_angle_d3.0541796
X-RAY DIFFRACTIONf_chiral_restr0.03323
X-RAY DIFFRACTIONf_plane_restr0.001366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5523-2.71210.27831310.25922558
2.7121-2.92150.25231370.21962563
2.9215-3.21530.26681330.21082568
3.2153-3.68010.20991380.18222581
3.6801-4.6350.18251340.1542607
4.635-35.5120.16871450.1582717
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.80265.37746.0126.67425.28636.7809-0.3010.0781-0.1023-0.13890.4011-0.5567-0.87030.2439-0.29430.50230.00670.03750.55820.04560.4261-39.817552.48872.8625
21.2789-0.7638-1.88753.7350.09383.12660.6377-0.02671.08340.0007-0.4304-0.7209-0.0570.404-0.0220.5365-0.0909-0.05710.4598-0.00890.3763-39.569449.72514.6863
32.8101-2.9055-0.04753.24450.78783.4535-0.28890.06210.03670.1534-0.0150.0258-0.0887-0.21230.1460.4167-0.0432-0.05360.5261-0.00220.1905-44.676841.74569.1456
45.4448-5.5298-5.38885.72275.68935.69580.58750.5555-0.0224-0.6257-0.0034-0.5647-0.58470.4081-0.49980.523-0.1901-0.1130.9050.12520.4743-27.136142.9823.3966
51.8629-0.89912.38761.4269-0.35424.18120.12790.5839-0.119-0.1206-0.1266-0.0140.07820.4358-0.00140.377-0.0220.03040.47420.0130.19-43.850436.05861.1893
67.35610.39185.00982.5721-0.17123.38290.0774-0.1739-0.4920.29710.1693-0.13070.1418-0.0627-0.09190.3682-0.04040.00760.39720.0670.2124-41.980232.108211.4586
74.08-4.42315.55517.3463-4.34039.2544-0.8866-1.73991.12791.60940.20320.0398-1.4678-0.76020.65340.98330.1335-0.17880.8569-0.18620.5701-40.906643.021324.6514
89.61654.5267-5.5334.9858-6.10339.26310.1662-0.80871.24653.0255-0.80050.0521-3.0074-1.40270.34921.08960.1962-0.13240.9546-0.29270.6088-52.273652.792820.1272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 299 through 331 )A299 - 331
2X-RAY DIFFRACTION2chain 'A' and (resid 332 through 370 )A332 - 370
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 397 )A371 - 397
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 409 )A398 - 409
5X-RAY DIFFRACTION5chain 'A' and (resid 410 through 494 )A410 - 494
6X-RAY DIFFRACTION6chain 'A' and (resid 495 through 522 )A495 - 522
7X-RAY DIFFRACTION7chain 'A' and (resid 523 through 540 )A523 - 540
8X-RAY DIFFRACTION8chain 'C' and (resid 742 through 751 )C742 - 751

+
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