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- PDB-4gnt: Complex of ChREBP and 14-3-3beta -

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Basic information

Entry
Database: PDB / ID: 4gnt
TitleComplex of ChREBP and 14-3-3beta
Components
  • 14-3-3 protein beta/alpha
  • Carbohydrate-responsive element-binding protein
KeywordsPROTEIN BINDING / protein-protein complex / alpha-alpha helical / protein-protein interaction / 14-3-3 / cytoplasm/nucleus
Function / homology
Function and homology information


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 / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo ...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 / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo / Negative regulation of MAPK pathway / glucose mediated signaling pathway / TP53 Regulates Metabolic Genes / mTORC1-mediated signalling / RAF activation / positive regulation of transcription from RNA polymerase II promoter by glucose / MAP2K and MAPK activation / Rap1 signalling / positive regulation of fatty acid biosynthetic process / negative regulation of oxidative phosphorylation / negative regulation of G protein-coupled receptor signaling pathway / lipid biosynthetic process / negative regulation of protein import into nucleus / protein phosphatase inhibitor activity / protein kinase inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phosphoserine residue binding / fatty acid homeostasis / protein targeting / positive regulation of lipid biosynthetic process / energy homeostasis / protein sequestering activity / positive regulation of glycolytic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / melanosome / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / 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 ...: / 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 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Carbohydrate-responsive element-binding protein / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsZhang, H. / Huang, N.
CitationJournal: To be Published
Title: Crystal Structure of Carbohydrate Response Element Binding Protein (ChREBP) in complex with 14-3-3b
Authors: Ge, Q. / Huang, N. / Zhang, H. / Uyeda, K.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)31,3936
Polymers31,0092
Non-polymers3844
Water1,27971
1
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)62,78612
Polymers62,0184
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area6800 Å2
ΔGint-107 kcal/mol
Surface area25350 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)125,57224
Polymers124,0358
Non-polymers1,53716
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 area15970 Å2
ΔGint-228 kcal/mol
Surface area48330 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-47 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.864, 115.864, 59.470
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-403-

HOH

21A-409-

HOH

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Components

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


Mass: 28240.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ywhab / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV8
#2: Protein/peptide Carbohydrate-responsive element-binding protein / ChREBP / MLX interactor / MLX-interacting protein-like / Williams-Beuren syndrome chromosomal ...ChREBP / MLX interactor / MLX-interacting protein-like / Williams-Beuren syndrome chromosomal region 14 protein homolog


Mass: 2768.206 Da / Num. of mol.: 1 / Fragment: UNP residues 117-137 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q99MZ3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM sodium citrate, 200mM sodium/potassium tartrate, 2.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorDate: Mar 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→33.7 Å / Num. all: 29835 / Num. obs: 28628 / % possible obs: 3.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→33.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.335 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23866 773 5 %RANDOM
Rwork0.19742 ---
obs0.1994 14627 95.33 %-
all-29835 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.41→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 20 71 2149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7961.9672864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8625254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83124.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15415414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3391515
X-RAY DIFFRACTIONr_chiral_restr0.0510.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021577
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7351.51267
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.69722037
X-RAY DIFFRACTIONr_scbond_it9.6983859
X-RAY DIFFRACTIONr_scangle_it15.3274.5827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.411→2.474 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 54 -
Rwork0.32 949 -
obs--86.69 %
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)
10.43170.06970.01230.9359-0.49520.633-0.043-0.0421-0.0999-0.021-0.0156-0.0323-0.16280.04020.05860.0851-0.02310.02120.02440.03620.0992-21.155540.81438.2397
21.9323-1.8578-4.3525.6568.838813.2211-0.168-0.05340.15760.0946-0.5052-0.6696-0.34090.06320.67320.0965-0.1341-0.13520.06140.24250.4793-9.651849.506413.5609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 232
2X-RAY DIFFRACTION2B117 - 137

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