[English] 日本語
Yorodumi
- PDB-6kz5: Crystal Structure Analysis of the Csn-B-bounded NUR77 Ligand bind... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kz5
TitleCrystal Structure Analysis of the Csn-B-bounded NUR77 Ligand binding Domain
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION / NR4A1 / Nur77
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear 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
Similarity search - Domain/homology
Chem-E4L / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.45 Å
AuthorsHong, W. / Chen, H. / Wu, Q. / Lin, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression.
Authors: Yang, P.B. / Hou, P.P. / Liu, F.Y. / Hong, W.B. / Chen, H.Z. / Sun, X.Y. / Li, P. / Zhang, Y. / Ju, C.Y. / Luo, L.J. / Wu, S.F. / Zhou, J.X. / Wang, Z.J. / He, J.P. / Li, L. / Zhao, T.J. / ...Authors: Yang, P.B. / Hou, P.P. / Liu, F.Y. / Hong, W.B. / Chen, H.Z. / Sun, X.Y. / Li, P. / Zhang, Y. / Ju, C.Y. / Luo, L.J. / Wu, S.F. / Zhou, J.X. / Wang, Z.J. / He, J.P. / Li, L. / Zhao, T.J. / Deng, X. / Lin, T. / Wu, Q.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression
Authors: Yang, P. / Hou, P. / Liu, F. / Hong, W. / Chen, H. / Sun, X. / Li, P. / Zhang, Y. / Ju, C. / Luo, L. / Wu, S. / Zhou, J. / Wang, Z. / He, J. / Li, L. / Zhao, T. / Deng, X. / Lin, T. / Wu, Q.
#2: Journal: Nat. Chem. Biol. / Year: 2012
Title: The orphan nuclear receptor Nur77 regulates LKB1 localization and activates AMPK.
Authors: Zhan, Y.Y. / Chen, Y. / Zhang, Q. / Zhuang, J.J. / Tian, M. / Chen, H.Z. / Zhang, L.R. / Zhang, H.K. / He, J.P. / Wang, W.J. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A.Z. / Xin, Y.Z. / ...Authors: Zhan, Y.Y. / Chen, Y. / Zhang, Q. / Zhuang, J.J. / Tian, M. / Chen, H.Z. / Zhang, L.R. / Zhang, H.K. / He, J.P. / Wang, W.J. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A.Z. / Xin, Y.Z. / Li, T.Y. / Yang, J.Y. / Zheng, Z.H. / Yu, C.D. / Lin, S.C. / Chang, C. / Huang, P.Q. / Lin, T. / Wu, Q.
History
DepositionSep 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor subfamily 4 group A member 1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8133
Polymers57,4912
Non-polymers3221
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-16 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.589, 76.099, 127.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nuclear receptor subfamily 4 group A member 1 / Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR ...Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR / Orphan nuclear receptor TR3 / ST-59 / Testicular receptor 3


Mass: 28745.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22736
#2: Chemical ChemComp-E4L / ethyl 2-[2-octanoyl-3,5-bis(oxidanyl)phenyl]ethanoate / ethyl 2-(3,5-dihydroxy-2-octanoylphenyl)acetate


Mass: 322.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 ...Details: Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 mM sodium citrate (pH 4.6), 22% glycerol and 5% PEG4000. Crystals appeared after 24-48 h and were ready for data collection in 7 d.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: SDMS / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.45→50 Å / Num. obs: 4038 / % possible obs: 91.2 % / Redundancy: 2.4 % / CC1/2: 0.914 / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.514
Reflection shellResolution: 4.5→4.58 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 197 / CC1/2: 0.656

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3E

3v3e


Resolution: 4.45→33.28 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.745 / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3079 154 4.5 %RANDOM
Rwork0.2457 ---
obs0.2485 3241 70.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.17 Å2 / Biso mean: 27.911 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.28 Å20 Å20 Å2
2---0.4 Å20 Å2
3----7.88 Å2
Refinement stepCycle: final / Resolution: 4.45→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 23 0 3657
Biso mean--69.45 --
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133740
X-RAY DIFFRACTIONr_bond_other_d0.0110.0173635
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.6315066
X-RAY DIFFRACTIONr_angle_other_deg1.4341.578410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2421.202183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84115648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3731528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
LS refinement shellResolution: 4.45→4.562 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.224 3 -
Rwork0.224 168 -
obs--52.29 %

+
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://pdbjlvh1.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