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- PDB-5x07: Crystal structure of FOXA2 DNA binding domain bound to a full con... -

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Basic information

Entry
Database: PDB / ID: 5x07
TitleCrystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site
Components
  • DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
  • Hepatocyte nuclear factor 3-beta
KeywordsDNA BINDING PROTEIN/DNA / FOXA2 / Forkhead domain / Consensus binding site / Isothermal Titration Calorimetry / ITC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / negative regulation of epithelial to mesenchymal transition / regulation of insulin secretion involved in cellular response to glucose stimulus ...negative regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / negative regulation of epithelial to mesenchymal transition / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / positive regulation of gastrulation / Formation of axial mesoderm / dopaminergic neuron differentiation / cell fate specification / regulation of blood coagulation / Regulation of gene expression in beta cells / anatomical structure morphogenesis / adult locomotory behavior / negative regulation of DNA-binding transcription factor activity / sequence-specific double-stranded DNA binding / cell junction / chromatin organization / nucleic acid binding / cell differentiation / transcription cis-regulatory region 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 domain specific binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD ...Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Hepatocyte nuclear factor 3-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsLi, J. / Guo, M. / Zhou, Z. / Jiang, L. / Chen, X. / Qu, L. / Wu, D. / Chen, Z. / Chen, L. / Chen, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81372904 China
National Natural Science Foundation of China81570537 China
National Natural Science Foundation of China81272971 China
CitationJournal: Biochemistry / Year: 2017
Title: Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site
Authors: Li, J. / Machado, A.C.D. / Guo, M. / Sagendorf, J.M. / Zhou, Z. / Jiang, L. / Chen, X. / Wu, D. / Qu, L. / Chen, Z. / Chen, L. / Rohs, R. / Chen, Y.
History
DepositionJan 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Derived calculations / Category: pdbx_validate_symm_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
E: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
F: Hepatocyte nuclear factor 3-beta
A: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
B: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
C: Hepatocyte nuclear factor 3-beta
G: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
H: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
I: Hepatocyte nuclear factor 3-beta
J: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
K: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
L: Hepatocyte nuclear factor 3-beta


Theoretical massNumber of molelcules
Total (without water)88,73912
Polymers88,73912
Non-polymers00
Water0
1
D: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
E: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
F: Hepatocyte nuclear factor 3-beta


Theoretical massNumber of molelcules
Total (without water)22,1853
Polymers22,1853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-27 kcal/mol
Surface area9980 Å2
MethodPISA
2
A: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
B: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
C: Hepatocyte nuclear factor 3-beta


Theoretical massNumber of molelcules
Total (without water)22,1853
Polymers22,1853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-27 kcal/mol
Surface area9790 Å2
MethodPISA
3
G: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
H: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
I: Hepatocyte nuclear factor 3-beta


Theoretical massNumber of molelcules
Total (without water)22,1853
Polymers22,1853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-26 kcal/mol
Surface area9920 Å2
MethodPISA
4
J: DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')
K: DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')
L: Hepatocyte nuclear factor 3-beta


Theoretical massNumber of molelcules
Total (without water)22,1853
Polymers22,1853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-26 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.126, 71.932, 72.155
Angle α, β, γ (deg.)90.00, 103.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain
DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)-3')


Mass: 4860.159 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain
DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)-3')


Mass: 4932.272 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Hepatocyte nuclear factor 3-beta / HNF-3B / Forkhead box protein A2 / Transcription factor 3B / TCF-3B


Mass: 12392.217 Da / Num. of mol.: 4 / Fragment: UNP residues 157-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA2, HNF3B, TCF3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y261

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 80mM Mg (OAc)2, 50mM MES buffer, 16%-20% PEG4K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.796→33.64 Å / Num. obs: 178752 / % possible obs: 96.8 % / Redundancy: 7.5 % / Net I/σ(I): 19.47

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data processing
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.796→33.637 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.22
RfactorNum. reflection% reflection
Rfree0.2785 1994 8.49 %
Rwork0.2398 --
obs0.2431 23493 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.796→33.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 2600 0 0 5405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055851
X-RAY DIFFRACTIONf_angle_d1.1088464
X-RAY DIFFRACTIONf_dihedral_angle_d28.8522348
X-RAY DIFFRACTIONf_chiral_restr0.042900
X-RAY DIFFRACTIONf_plane_restr0.007640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7961-2.8660.41071190.37771280X-RAY DIFFRACTION81
2.866-2.94340.42961420.36851538X-RAY DIFFRACTION98
2.9434-3.030.3751450.36771545X-RAY DIFFRACTION98
3.03-3.12770.37991440.32681572X-RAY DIFFRACTION98
3.1277-3.23940.37631450.30811544X-RAY DIFFRACTION98
3.2394-3.3690.31931400.28131529X-RAY DIFFRACTION97
3.369-3.52220.32331440.27541537X-RAY DIFFRACTION98
3.5222-3.70770.30491420.27161546X-RAY DIFFRACTION98
3.7077-3.93960.27221450.24161552X-RAY DIFFRACTION98
3.9396-4.24330.29051440.24011563X-RAY DIFFRACTION97
4.2433-4.66930.25041400.21151510X-RAY DIFFRACTION96
4.6693-5.34260.24941440.22511550X-RAY DIFFRACTION97
5.3426-6.72230.24361490.20481601X-RAY DIFFRACTION99
6.7223-33.6390.20761510.17211632X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 178.8931 Å / Origin y: 40.393 Å / Origin z: 185.4466 Å
111213212223313233
T0.4063 Å20.0158 Å2-0.0171 Å2-0.5418 Å2-0.0768 Å2--0.4898 Å2
L-0.1341 °2-0.1802 °2-0.1647 °2-0.2348 °2-0.1064 °2--0.1634 °2
S-0.0015 Å °-0.1745 Å °0.059 Å °-0.1026 Å °0.1313 Å °-0.0894 Å °0.0255 Å °-0.0465 Å °0.2182 Å °
Refinement TLS groupSelection details: all

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