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- PDB-5f74: Crystal structure of ChREBP:14-3-3 complex bound with AMP -

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Basic information

Entry
Database: PDB / ID: 5f74
TitleCrystal structure of ChREBP:14-3-3 complex bound with AMP
Components
  • 14-3-3 protein beta/alpha
  • Carbohydrate-responsive element-binding protein
KeywordsTRANSCRIPTION / ChREBP / 14-3-3 / AMP / Allosteric
Function / homology
Function and homology information


PKA-mediated phosphorylation of key metabolic factors / : / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / carbohydrate response element binding / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Regulation of localization of FOXO transcription factors / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / regulation of cell cycle => GO:0051726 / Activation of BAD and translocation to mitochondria ...PKA-mediated phosphorylation of key metabolic factors / : / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / carbohydrate response element binding / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Regulation of localization of FOXO transcription factors / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / regulation of cell cycle => GO:0051726 / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo / Negative regulation of MAPK pathway / negative regulation of protein dephosphorylation / glucose mediated signaling pathway / TP53 Regulates Metabolic Genes / RAF activation / mTORC1-mediated signalling / MAP2K and MAPK activation / Rap1 signalling / cytoplasmic sequestering of protein / negative regulation of G protein-coupled receptor signaling pathway / positive regulation of fatty acid biosynthetic process / negative regulation of oxidative phosphorylation / regulation of glycolytic process / protein kinase inhibitor activity / transcription factor binding / phosphoserine residue binding / protein targeting / response to glucose / fatty acid homeostasis / energy homeostasis / negative regulation of peptidyl-serine phosphorylation / positive regulation of lipid biosynthetic process / transcription repressor complex / positive regulation of glycolytic process / cellular response to glucose stimulus / phosphoprotein binding / intracellular protein transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / melanosome / glucose homeostasis / transcription regulator complex / sequence-specific DNA 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 heterodimerization activity / protein domain specific binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / protein-containing complex binding / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Helix-loop-helix DNA-binding domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily ...Helix-loop-helix DNA-binding domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Carbohydrate-responsive element-binding protein / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJung, H. / Uyeda, K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Metabolite Regulation of Nuclear Localization of Carbohydrate-response Element-binding Protein (ChREBP): ROLE OF AMP AS AN ALLOSTERIC INHIBITOR.
Authors: Sato, S. / Jung, H. / Nakagawa, T. / Pawlosky, R. / Takeshima, T. / Lee, W.R. / Sakiyama, H. / Laxman, S. / Wynn, R.M. / Tu, B.P. / MacMillan, J.B. / De Brabander, J.K. / Veech, R.L. / Uyeda, K.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein beta/alpha
B: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1223
Polymers50,7742
Non-polymers3471
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-6 kcal/mol
Surface area12970 Å2
MethodPISA
2
A: 14-3-3 protein beta/alpha
B: Carbohydrate-responsive element-binding protein
hetero molecules

A: 14-3-3 protein beta/alpha
B: Carbohydrate-responsive element-binding protein
hetero molecules

A: 14-3-3 protein beta/alpha
B: Carbohydrate-responsive element-binding protein
hetero molecules

A: 14-3-3 protein beta/alpha
B: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,48712
Polymers203,0988
Non-polymers1,3894
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area16230 Å2
ΔGint-60 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.620, 115.620, 59.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

#1: Protein 14-3-3 protein beta/alpha / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28118.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ywhab / Plasmid: pET Duet / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV8
#2: Protein Carbohydrate-responsive element-binding protein / / ChREBP / Class D basic helix-loop-helix protein 14 / bHLHd14 / MLX interactor / MLX-interacting ...ChREBP / Class D basic helix-loop-helix protein 14 / bHLHd14 / MLX interactor / MLX-interacting protein-like / WS basic-helix-loop-helix leucine zipper protein / WS-bHLH / Williams-Beuren syndrome chromosomal region 14 protein


Mass: 22656.010 Da / Num. of mol.: 1 / Fragment: UNP residues 1-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mlxipl, Wbscr14 / Plasmid: pET Duet / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VIP2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate 200 mM sodium potassium tartrate 2.2 M ammonium sulfate
PH range: 6.2 -7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 17340 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNT

4gnt


Resolution: 2.35→41.419 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 867 5.01 %
Rwork0.1881 --
obs0.1914 17314 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→41.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 23 45 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082081
X-RAY DIFFRACTIONf_angle_d0.9952804
X-RAY DIFFRACTIONf_dihedral_angle_d15.914785
X-RAY DIFFRACTIONf_chiral_restr0.039310
X-RAY DIFFRACTIONf_plane_restr0.004355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.49730.30811380.26082671X-RAY DIFFRACTION100
2.4973-2.69010.30061480.23942685X-RAY DIFFRACTION100
2.6901-2.96070.27241560.22162691X-RAY DIFFRACTION100
2.9607-3.3890.28941390.21832718X-RAY DIFFRACTION100
3.389-4.26910.2141400.16232764X-RAY DIFFRACTION100
4.2691-41.42550.24811460.16632918X-RAY DIFFRACTION100

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