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- PDB-4cyc: CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPT... -

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Basic information

Entry
Database: PDB / ID: 4cyc
TitleCRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS
Components
  • 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'
  • 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'
  • HOMEOBOX PROTEIN EXTRADENTICLE
  • HOMEOTIC PROTEIN ULTRABITHORAXHomeosis
KeywordsTRANSCRIPTION / HOX / PBC / DNA PROTEIN COMPLEX
Function / homology
Function and homology information


dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / salivary gland boundary specification / haltere development / oenocyte development / mesodermal cell fate specification / specification of segmental identity, thorax ...dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / salivary gland boundary specification / haltere development / oenocyte development / mesodermal cell fate specification / specification of segmental identity, thorax / open tracheal system development / imaginal disc-derived leg morphogenesis / somatic muscle development / muscle cell fate specification / polytene chromosome band / endoderm formation / eye development / regulation of cell fate specification / peripheral nervous system development / cell fate determination / anterior/posterior pattern specification / midgut development / transcription factor binding / neuron development / embryonic organ development / cis-regulatory region sequence-specific DNA binding / transcription repressor complex / transcription coregulator binding / protein-DNA complex / transcription coregulator activity / animal organ morphogenesis / brain development / RNA polymerase II transcription regulator complex / heart development / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / 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 heterodimerization activity / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox KN domain / Homeobox KN domain / 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) / Homeobox protein extradenticle / Homeotic protein ultrabithorax
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsFoos, N. / Mate, M.J. / Ortiz-Lombardia, M.
CitationJournal: Structure / Year: 2015
Title: A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode.
Authors: Foos, N. / Maurel-Zaffran, C. / Mate, M.J. / Vincentelli, R. / Hainaut, M. / Berenger, H. / Pradel, J. / Saurin, A.J. / Ortiz-Lombardia, M. / Graba, Y.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOMEOTIC PROTEIN ULTRABITHORAX
B: HOMEOBOX PROTEIN EXTRADENTICLE
C: 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'
D: 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)29,4954
Polymers29,4954
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28.5 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.707, 97.707, 73.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HOMEOTIC PROTEIN ULTRABITHORAX / Homeosis


Mass: 11459.246 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN WITH HX AND UBDA, RESIDUES 233-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: UBXIVA PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P83949
#2: Protein HOMEOBOX PROTEIN EXTRADENTICLE / / DPBX / HOMEOTIC PROTEIN EXTRADENTICLE


Mass: 8857.946 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN RESIDUES 238-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: EXD2 PETG20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P40427
#3: DNA chain 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'


Mass: 4537.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
#4: DNA chain 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'


Mass: 4640.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST METHIONINE FROM EXPRESSION VECTOR FIRST GLYCINE FROM EXPRESSION VECTOR

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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: 3.48 Å3/Da / Density % sol: 68.5 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M AMMONIUM PHOSPHATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.3853
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3853 Å / Relative weight: 1
ReflectionResolution: 2.36→84.62 Å / Num. obs: 17094 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 10.8 % / Biso Wilson estimate: 83.97 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 41.2
Reflection shellResolution: 2.36→2.37 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BZL

4bzl
PDB Unreleased entry


Resolution: 2.36→25 Å / Cor.coef. Fo:Fc: 0.9425 / Cor.coef. Fo:Fc free: 0.9429 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 863 5.07 %RANDOM
Rwork0.2121 ---
obs0.2128 17038 99.94 %-
Displacement parametersBiso mean: 87.18 Å2
Baniso -1Baniso -2Baniso -3
1--3.8322 Å20 Å20 Å2
2---3.8322 Å20 Å2
3---7.6643 Å2
Refine analyzeLuzzati coordinate error obs: 0.828 Å
Refinement stepCycle: LAST / Resolution: 2.36→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 609 0 68 1756
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091807HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882556HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d572SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes190HARMONIC5
X-RAY DIFFRACTIONt_it1807HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion21.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1909SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.5 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2745 141 5.18 %
Rwork0.2472 2579 -
all0.2487 2720 -
obs--99.94 %
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)
14.6769-0.6148-1.66765.6381-1.387611.0884-0.1314-0.06290.73130.76990.3419-0.2977-1.48590.399-0.21050.103-0.1121-0.1088-0.4696-0.0142-0.1948-41.301615.95328.9342
23.8978-1.02620.87953.09770.298816.42340.12240.4397-0.0097-0.4562-0.14230.0803-0.67650.05870.01990.2836-0.1484-0.0454-0.24350.0368-0.177-46.64485.818-16.1441
34.08143.3726-1.647713.6297-4.801914.6098-0.43350.06030.4909-0.51410.1258-0.525-1.12380.53960.30770.0777-0.2833-0.1139-0.29720.0059-0.0396-39.299613.20770.0095
4-0.0594-1.2302-0.47574.4397-3.300912.81310.0611-0.0513-0.0593-0.3246-0.2167-0.4859-0.32390.29740.15560.2032-0.2147-0.0137-0.25090.02460.0554-41.96687.5963-2.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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