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- PDB-2a07: Crystal Structure of Foxp2 bound Specifically to DNA. -

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Basic information

Entry
Database: PDB / ID: 2a07
TitleCrystal Structure of Foxp2 bound Specifically to DNA.
Components
  • 5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3'
  • 5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3'
  • Forkhead box protein P2FOX proteins
KeywordsTranscription/DNA / Forkhead / Double-Helix / Swapping / Homodimer / Monomer / Winged-Helix / Magnesium / Transcription-DNA COMPLEX
Function / homology
Function and homology information


caudate nucleus development / putamen development / cerebral cortex development / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / negative regulation of DNA-templated transcription / chromatin ...caudate nucleus development / putamen development / cerebral cortex development / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / identical protein binding / metal ion binding / nucleus
Similarity search - Function
: / FOXP, coiled-coil domain / FOXP coiled-coil domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Zinc finger C2H2 type domain signature. ...: / FOXP, coiled-coil domain / FOXP coiled-coil domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Zinc finger C2H2 type domain signature. / 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) / Forkhead box protein P2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStroud, J.C. / Wu, Y. / Bates, D.L. / Han, A. / Nowick, K. / Paabo, S. / Tong, H. / Chen, L.
CitationJournal: Structure / Year: 2006
Title: Structure of the Forkhead Domain of FOXP2 Bound to DNA.
Authors: Stroud, J.C. / Wu, Y. / Bates, D.L. / Han, A. / Nowick, K. / Paabo, S. / Tong, H. / Chen, L.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3'
B: 5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3'
C: 5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3'
D: 5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3'
F: Forkhead box protein P2
G: Forkhead box protein P2
H: Forkhead box protein P2
I: Forkhead box protein P2
J: Forkhead box protein P2
K: Forkhead box protein P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,06016
Polymers91,91510
Non-polymers1466
Water10,467581
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.542, 124.210, 67.666
Angle α, β, γ (deg.)90.00, 110.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3'


Mass: 6389.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA is Synthesized by Solid Phase Method
#2: DNA chain 5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3'


Mass: 6491.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA is Synthesized by Solid Phase Method
#3: Protein
Forkhead box protein P2 / FOX proteins / CAG repeat protein 44 / Trinucleotide repeat-containing gene 10 protein


Mass: 11025.630 Da / Num. of mol.: 6 / Fragment: Foxp2 Forkhead Domain / Mutation: D502I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXP2, CAGH44, TNRC10 / Production host: Escherichia coli (E. coli) / References: UniProt: O15409
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.99 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.68
Details: BTP, Sodium Chloride, PEG 3k, Magnesium Chloride, Sodium Azide, pH 6.68, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1BTP11
2Sodium Chloride11
3PEG 3k11
4Magnesium Chloride11
5Sodium Azide11
6H2O11
7Sodium Chloride12
8PEG 3k12
9Magnesium Chloride12
10H2O12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 81978 / Num. obs: 79203 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 28.46
Reflection shellResolution: 1.9→1.97 Å / % possible all: 8.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2436 7443 Random
Rwork0.2224 --
all0.2311 81978 -
obs0.2224 73908 -
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 1710 6 581 6446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005852
X-RAY DIFFRACTIONc_angle_deg1.06712
X-RAY DIFFRACTIONc_dihedral_angle_d18.99112
X-RAY DIFFRACTIONc_improper_angle_d0.95273

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