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- PDB-9gcp: ChREBP/14-3-3 complex stabilized by AMP -

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Basic information

Entry
Database: PDB / ID: 9gcp
TitleChREBP/14-3-3 complex stabilized by AMP
Components
  • 14-3-3 protein beta/alpha, N-terminally processed
  • Carbohydrate-responsive element-binding protein
KeywordsTRANSCRIPTION / AMP / carbohydrate and lipid homeostasis / lipogenesis / ChREBP / transcription factor / allosteric regulation
Function / homology
Function and homology information


carbohydrate response element binding / glucose mediated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / PKA-mediated phosphorylation of key metabolic factors / PP2A-mediated dephosphorylation of key metabolic factors / positive regulation of transcription from RNA polymerase II promoter by glucose / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / ChREBP activates metabolic gene expression / positive regulation of fatty acid biosynthetic process ...carbohydrate response element binding / glucose mediated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / PKA-mediated phosphorylation of key metabolic factors / PP2A-mediated dephosphorylation of key metabolic factors / positive regulation of transcription from RNA polymerase II promoter by glucose / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / ChREBP activates metabolic gene expression / positive regulation of fatty acid biosynthetic process / MTOR signalling / ARMS-mediated activation / negative regulation of oxidative phosphorylation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / triglyceride homeostasis / negative regulation of G protein-coupled receptor signaling pathway / Frs2-mediated activation / protein phosphatase inhibitor activity / negative regulation of protein import into nucleus / DNA-binding transcription activator activity / lipid biosynthetic process / protein kinase inhibitor activity / negative regulation of signal transduction by p53 class mediator / energy homeostasis / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / anatomical structure morphogenesis / Activation of BAD and translocation to mitochondria / fatty acid homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of lipid biosynthetic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / transcription repressor complex / Transcriptional and post-translational regulation of MITF-M expression and activity / protein sequestering activity / positive regulation of glycolytic process / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Negative regulation of MAPK pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / melanosome / intracellular protein localization / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Helix-loop-helix DNA-binding domain / 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 / 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 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 14-3-3 protein beta/alpha / Carbohydrate-responsive element-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMoschref, M. / Heimhalt, M. / Pysik, T. / Menzer, W.M. / Basquin, J. / Margulies, C.E. / Ladurner, A.G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Bavarian State Ministry for Education, Culture, Science and Arts41-6663a1213/2-M4-2110-0006 Germany
Citation
Journal: To Be Published
Title: Glucose-6-phosphate functions as a selective receptor agonist for the sugar tolerance transcription factor ChREBP
Authors: Moschref, M. / Heimhalt, M. / Pysik, T. / Menzer, W.M. / Basquin, J. / Margulies, C.E. / Ladurner, A.G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein beta/alpha, N-terminally processed
B: Carbohydrate-responsive element-binding protein
C: 14-3-3 protein beta/alpha, N-terminally processed
D: Carbohydrate-responsive element-binding protein
E: 14-3-3 protein beta/alpha, N-terminally processed
F: Carbohydrate-responsive element-binding protein
G: 14-3-3 protein beta/alpha, N-terminally processed
H: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,75212
Polymers116,3638
Non-polymers1,3894
Water00
1
A: 14-3-3 protein beta/alpha, N-terminally processed
B: Carbohydrate-responsive element-binding protein
E: 14-3-3 protein beta/alpha, N-terminally processed
F: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8766
Polymers58,1824
Non-polymers6942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 14-3-3 protein beta/alpha, N-terminally processed
D: Carbohydrate-responsive element-binding protein
G: 14-3-3 protein beta/alpha, N-terminally processed
H: Carbohydrate-responsive element-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8766
Polymers58,1824
Non-polymers6942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.515, 80.279, 244.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 3 through 7 and (name N...
d_2ens_1(chain "C" and ((resid 3 through 7 and (name N...
d_3ens_1(chain "E" and ((resid 3 through 7 and (name N...
d_4ens_1(chain "G" and ((resid 3 through 7 and (name N...
d_1ens_2(chain "B" and (resid 117 through 125 or (resid 126...
d_2ens_2(chain "D" and (resid 117 through 125 or (resid 126...
d_3ens_2(chain "F" and (resid 117 through 125 or (resid 126...
d_4ens_2(chain "H" and (resid 117 through 132 or (resid 133...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETLYSLYSAA3 - 701 - 68
d_12ens_1ASNASNTHRTHRAA74 - 23172 - 229
d_13ens_1AMPAMPAMPAMPGL301
d_21ens_1METMETLYSLYSCC3 - 701 - 68
d_22ens_1ASNASNTHRTHRCC74 - 23172 - 229
d_23ens_1AMPAMPAMPAMPAI301
d_31ens_1METMETTHRTHREE3 - 2311 - 229
d_32ens_1AMPAMPAMPAMPEK301
d_41ens_1METMETLYSLYSGG3 - 701 - 68
d_42ens_1ASNASNTHRTHRGG74 - 23172 - 229
d_43ens_1AMPAMPAMPAMPCJ301
d_11ens_2ARGARGVALVALBB117 - 1351 - 19
d_21ens_2ARGARGVALVALDD117 - 1351 - 19
d_31ens_2ARGARGVALVALFF117 - 1351 - 19
d_41ens_2ARGARGVALVALHH117 - 1351 - 19

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99621687378004, 0.068788716103519, 0.053104170577691), (0.070634645037925, -0.99693276765179, -0.033701686938745), (0.050622991972831, 0.037325183442019, -0.99802011170354)-3.2228606718925, -2.5069766187874, 60.571346482776
2given(-0.99964600958264, -0.024785574086493, -0.0096711345101742), (-0.025608522479725, 0.99494371931391, 0.097114360288349), (0.0072151993677485, 0.097327646200927, -0.99522624070262)-26.848551120582, -2.7087572387852, 60.777249844094
3given(-0.99756704284953, 0.027196577646425, -0.064189883819597), (-0.017457414109477, -0.98888181575828, -0.1476752963607), (-0.067492471528768, -0.14619541930899, 0.98695069059199)-25.295311828203, -1.5750884200656, 1.0753903606202
4given(0.99475159730449, 0.051190598518214, 0.088593353495124), (0.050017211196004, -0.99862937700331, 0.015415770177443), (0.089261067909472, -0.010903669535363, -0.99594857886656)-3.2046113076925, -3.5174131969041, 62.443982240069
5given(-0.99968352914857, -0.0059884456947059, -0.024433175545025), (-0.0075552608971584, 0.99788608003944, 0.064546799272333), (0.023994990765331, 0.064710971107599, -0.99761552245165)-27.221348780112, -2.2637627589565, 61.677912866144
6given(-0.99590252945005, -0.0311542583199, -0.084897373478426), (0.036552234160052, -0.9973573095142, -0.0627879871991), (-0.082716902824677, -0.065633903945618, 0.99440942505587)-24.049072715765, -0.84650601552802, -0.94703375350576

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Components

#1: Protein
14-3-3 protein beta/alpha, N-terminally processed


Mass: 26479.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Variant: beta / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31946
#2: Protein/peptide
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: 2611.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NP71
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM MES ph 6.0 2.2M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→48.6 Å / Num. obs: 68910 / % possible obs: 99.69 % / Redundancy: 7 % / Biso Wilson estimate: 78.84 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.97
Reflection shellResolution: 2.59→2.63 Å / Num. unique obs: 2618 / CC1/2: 0.27

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Processing

Software
NameVersionClassification
PHENIX1.21.1refinement
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→48.6 Å / SU ML: 0.4431 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2713 3453 5.02 %
Rwork0.2279 65376 -
obs0.2301 68829 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.54 Å2
Refinement stepCycle: LAST / Resolution: 2.59→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 92 0 7894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618026
X-RAY DIFFRACTIONf_angle_d0.94810874
X-RAY DIFFRACTIONf_chiral_restr0.04781226
X-RAY DIFFRACTIONf_plane_restr0.00771384
X-RAY DIFFRACTIONf_dihedral_angle_d18.31832952
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.8782013830352
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS4.2125136196495
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS4.4443889810267
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.65777964226105
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.65377120783466
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.75026209460265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.630.41291350.38032481X-RAY DIFFRACTION95.79
2.63-2.660.34741410.35672682X-RAY DIFFRACTION100
2.66-2.70.39841380.35112574X-RAY DIFFRACTION99.96
2.7-2.750.35381350.33562618X-RAY DIFFRACTION100
2.75-2.790.31831400.31572668X-RAY DIFFRACTION99.96
2.79-2.840.34721410.32282611X-RAY DIFFRACTION99.96
2.84-2.890.38671330.30512605X-RAY DIFFRACTION100
2.89-2.950.33631380.30512662X-RAY DIFFRACTION99.96
2.95-3.010.28051390.30282569X-RAY DIFFRACTION99.93
3.01-3.070.3381350.30352674X-RAY DIFFRACTION99.75
3.07-3.140.36411410.32569X-RAY DIFFRACTION99.93
3.14-3.220.41681370.29822671X-RAY DIFFRACTION99.96
3.22-3.310.38431340.28062599X-RAY DIFFRACTION99.89
3.31-3.410.33441380.26082612X-RAY DIFFRACTION99.85
3.41-3.520.34321400.24552602X-RAY DIFFRACTION99.93
3.52-3.640.29251380.22672679X-RAY DIFFRACTION99.96
3.64-3.790.23461400.22132566X-RAY DIFFRACTION99.96
3.79-3.960.28591360.23652633X-RAY DIFFRACTION99.93
3.96-4.170.23771400.20582635X-RAY DIFFRACTION99.75
4.17-4.430.21131360.19082602X-RAY DIFFRACTION99.82
4.43-4.770.27321360.19212623X-RAY DIFFRACTION99.82
4.77-5.250.25131460.21982629X-RAY DIFFRACTION99.89
5.25-6.010.28941350.23022600X-RAY DIFFRACTION99.85
6.01-7.560.24831420.22182619X-RAY DIFFRACTION100
7.57-48.60.18871390.16092593X-RAY DIFFRACTION98.52

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