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- PDB-6pax: CRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA COMPLEX RE... -

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Basic information

Entry
Database: PDB / ID: 6pax
TitleCRYSTAL STRUCTURE OF THE HUMAN PAX-6 PAIRED DOMAIN-DNA COMPLEX REVEALS A GENERAL MODEL FOR PAX PROTEIN-DNA INTERACTIONS
Components
  • (26 NUCLEOTIDE DNA) x 2
  • HOMEOBOX PROTEIN PAX-6
KeywordsGENE REGULATION/DNA / PAX / PAIRED DOMAIN / TRANSCRIPTION / PROTEIN-DNA INTERACTIONS / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


pancreatic A cell development / oligodendrocyte cell fate specification / forebrain-midbrain boundary formation / commitment of neuronal cell to specific neuron type in forebrain / cerebral cortex regionalization / type B pancreatic cell differentiation / habenula development / forebrain dorsal/ventral pattern formation / cornea development in camera-type eye / regulation of timing of cell differentiation ...pancreatic A cell development / oligodendrocyte cell fate specification / forebrain-midbrain boundary formation / commitment of neuronal cell to specific neuron type in forebrain / cerebral cortex regionalization / type B pancreatic cell differentiation / habenula development / forebrain dorsal/ventral pattern formation / cornea development in camera-type eye / regulation of timing of cell differentiation / HMG box domain binding / iris morphogenesis / Formation of the anterior neural plate / regulation of asymmetric cell division / positive regulation of epithelial cell differentiation / embryonic camera-type eye morphogenesis / co-SMAD binding / lacrimal gland development / protein localization to organelle / ventral spinal cord development / pituitary gland development / sensory organ development / dorsal/ventral axis specification / eye photoreceptor cell development / neuron fate commitment / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / eye development / cell fate determination / astrocyte differentiation / lens development in camera-type eye / signal transduction involved in regulation of gene expression / negative regulation of neuroblast proliferation / smoothened signaling pathway / positive regulation of neuroblast proliferation / histone acetyltransferase binding / negative regulation of neuron differentiation / blood vessel development / forebrain development / R-SMAD binding / Regulation of gene expression in beta cells / establishment of mitotic spindle orientation / neuroblast proliferation / salivary gland morphogenesis / RNA polymerase II core promoter sequence-specific DNA binding / keratinocyte differentiation / visual perception / axon guidance / regulation of cell migration / cellular response to leukemia inhibitory factor / animal organ morphogenesis / central nervous system development / transcription coregulator binding / chromatin DNA binding / brain development / negative regulation of neurogenesis / positive regulation of miRNA transcription / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / neuron migration / negative regulation of epithelial cell proliferation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / sequence-specific double-stranded DNA binding / glucose homeostasis / nervous system development / retina development in camera-type eye / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Paired box protein Pax-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsXu, H.E. / Rould, M.A. / Xu, W. / Epstein, J.A. / Maas, R.L. / Pabo, C.O.
CitationJournal: Genes Dev. / Year: 1999
Title: Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding.
Authors: Xu, H.E. / Rould, M.A. / Xu, W. / Epstein, J.A. / Maas, R.L. / Pabo, C.O.
History
DepositionApr 22, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 26 NUCLEOTIDE DNA
C: 26 NUCLEOTIDE DNA
A: HOMEOBOX PROTEIN PAX-6


Theoretical massNumber of molelcules
Total (without water)30,4953
Polymers30,4953
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.840, 61.686, 171.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain 26 NUCLEOTIDE DNA


Mass: 7996.180 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 26 NUCLEOTIDE DNA


Mass: 7978.152 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein HOMEOBOX PROTEIN PAX-6


Mass: 14520.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAX6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26367
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMprotein-DNA complex1drop
240 mMHEPES1drop
310 mMspermine1drop
410 mMdithiothreitol1drop
55 mMEDTA1drop
620 %PEG2001drop
740 mMHEPES1reservoir
810 mMspermine1reservoir
910 mMdithiothreitol1reservoir
105 mMEDTA1reservoir
1120 %PEG2001reservoir
12200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 20530 / Num. obs: 20530 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR
Starting model: PRD-DNA COMPLEX

Resolution: 2.5→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 7123245.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1241 9.9 %RANDOM
Rwork0.233 ---
obs0.233 12593 96.3 %-
all-12593 --
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.66 Å20 Å20 Å2
2--7.25 Å20 Å2
3----18.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 1166 0 84 2528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.344
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.489
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.393 182 9.2 %
Rwork0.375 1791 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROPARHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNAPARNDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.489

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