[English] 日本語
Yorodumi
- PDB-1lv2: Hepatocyte Nuclear Factor 4 is a Transcription Factor that Consti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lv2
TitleHepatocyte Nuclear Factor 4 is a Transcription Factor that Constitutively Binds Fatty Acids
ComponentsHepatocyte nuclear factor 4-gamma
KeywordsTRANSCRIPTION / diabetes / fatty acids / HNF4 / MODY / nuclear receptor / transcription factor
Function / homology
Function and homology information


chromatin => GO:0000785 / anatomical structure development / Regulation of gene expression in beta cells / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...chromatin => GO:0000785 / anatomical structure development / Regulation of gene expression in beta cells / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / centrosome / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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
PALMITIC ACID / Hepatocyte nuclear factor 4-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsWisely, B. / Miller, A.B. / Davis, R.G. / Spitzer, T. / Shearer, B. / Moore, J.T. / Johnson, R. / Sefler, A. / Willson, T.M. / Williams, S.P.
CitationJournal: Structure / Year: 2002
Title: Hepatocyte Nuclear Factor 4 Is a Transcription Factor that Constitutively Binds Fatty Acids.
Authors: Wisely, G.B. / Miller, A.B. / Davis, R.G. / Jr Thornquest, A.D. / Johnson, R. / Spitzer, T. / Sefler, A. / Shearer, B. / Moore, J.T. / Willson, T.M. / Williams, S.P.
History
DepositionMay 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatocyte nuclear factor 4-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1112
Polymers25,8551
Non-polymers2561
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.708, 152.708, 93.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

-
Components

#1: Protein Hepatocyte nuclear factor 4-gamma / HNF-4-gamma


Mass: 25854.926 Da / Num. of mol.: 1 / Fragment: HNF4g LBD (residues 103-328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4G / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q14541
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.27 Å3/Da / Density % sol: 76.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
210 mMTris1droppH8.0
30.1 mMEDTA1drop
4150 mM1dropNaCl
510 mMdithiothreitol1drop
65 %propane-diol1drop
70.75 Mammonium dihydrogen phosphate/diammonium hydrogen phosphate1reservoirpH5.0
810 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2000 / Details: bent silicon crystal
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→22.4 Å / Num. all: 15429 / Num. obs: 15108 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 15.8 % / Biso Wilson estimate: 67.547 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 36.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1846 / Rsym value: 0.4 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Num. obs: 18866 / % possible obs: 98.4 % / Num. measured all: 1308098
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.32

-
Processing

Software
NameVersionClassification
MAR345data collection
HKL-2000data reduction
SHARPphasing
CNS2000refinement
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS
Starting model: Built by fitting pieces of secondary structure into density.

Resolution: 2.7→19.92 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1086 7.2 %RANDOM
Rwork0.245 ---
all0.247 15429 --
obs0.247 15108 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1994 Å2 / ksol: 0.339487 e/Å3
Displacement parametersBiso mean: 71.2 Å2
Baniso -1Baniso -2Baniso -3
1--17.99 Å20 Å20 Å2
2---17.99 Å20 Å2
3---35.98 Å2
Refine analyzeLuzzati coordinate error free: 0.46 Å / Luzzati sigma a free: 0.59 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 18 14 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.672
X-RAY DIFFRACTIONc_scangle_it4.052.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 172 7.5 %
Rwork0.365 2120 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLM.PARPLM.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.675
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

+
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