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- PDB-1du0: ENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1du0
TitleENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX
Components
  • DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3')
  • ENGRAILED HOMEODOMAIN
KeywordsTRANSCRIPTION/DNA / homeodomain / DNA-binding protein / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / RSC-type complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / axon guidance / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / negative regulation of neuron apoptotic process / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsGrant, R.A. / Rould, M.A. / Klemm, J.D. / Pabo, C.O.
Citation
Journal: Biochemistry / Year: 2000
Title: Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A.
Authors: Grant, R.A. / Rould, M.A. / Klemm, J.D. / Pabo, C.O.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Engrailed homeodomain-DNA complex at 2.2 Angstroms resolution: A detailed view of the interface and comparison with other engrailed structures
Authors: Fraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O.
#2: Journal: Structure / Year: 1997
Title: Engrailed (gln50->lys) homeodomain-DNA complex at 1.9 Angstroms resolution: structural basis for enhanced affinity and altered specificity
Authors: Tucker-Kellogg, L. / Rould, M.A. / Chambers, K.A. / Ades, S.E. / Sauer, R.T.
#3: Journal: Biochemistry / Year: 1994
Title: Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50
Authors: Ades, S.E. / Sauer, R.T.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: Crystal structure of an engrailed homeodomain-DNA comples at 2.8 Angstroms resolution: a framework for understanding homeodomain-DNA interactions
Authors: Kissinger, C.A. / Liu, B. / Martin-Blanco, E. / Kornberg, T.B. / Pabo, C.O.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3')
D: DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3')
A: ENGRAILED HOMEODOMAIN
B: ENGRAILED HOMEODOMAIN


Theoretical massNumber of molelcules
Total (without water)26,6974
Polymers26,6974
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.900, 45.550, 71.620
Angle α, β, γ (deg.)90.00, 119.90, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 6387.157 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3')


Mass: 6494.248 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein ENGRAILED HOMEODOMAIN / HOMEOTIC PROTEIN ENGRAILED / SEGMENTATION POLARITY HOMEOBOX PROTEIN ENGRAILED


Mass: 6907.921 Da / Num. of mol.: 2 / Mutation: GLN50ALA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02836
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: bis-Tris-propane, PEG 400, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium acetate11
2bis-Tris-propane11
3PEG 40011
4PEG 40012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mM1drop
41 %PEG4001reservoir
50.25 Mammonium acetate1reservoir
3duplex DNA1dropdissolved in 3.5 micro litter of 3M ammonium acetate

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Data collection

DiffractionMean temperature: 128 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 24, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 23204 / Num. obs: 23204 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.039
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.351 / Num. unique all: 1697 / % possible all: 70.3
Reflection
*PLUS
Num. measured all: 115772
Reflection shell
*PLUS
% possible obs: 70.3 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2168 10.1 %RANDOM
Rwork0.234 ---
all0.237 23204 --
obs0.237 21566 89 %-
Displacement parametersBiso mean: 39.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 855 0 104 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d18.4
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_mcbond_it2.711.5
X-RAY DIFFRACTIONx_mcangle_it4.072
X-RAY DIFFRACTIONx_scbond_it4.82
X-RAY DIFFRACTIONx_scangle_it7.332.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 203 9 %
Rwork0.363 2044 -
obs--56.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOLDNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44

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