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- PDB-4uus: CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF -

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Basic information

Entry
Database: PDB / ID: 4uus
TitleCRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF
Components
  • 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3'
  • 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3'
  • HOMEOTIC PROTEIN EXTRADENTICLE
  • HOMEOTIC PROTEIN ULTRABITHORAX
KeywordsTRANSCRIPTION / HOMEODOMAIN / HOX PROTEIN / PBC PROTEIN / DNA PROTEIN COMPLEX / TRANSCRIPTION FACTOR
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 / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor 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: 2.55 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
DepositionJul 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: HOMEOTIC PROTEIN EXTRADENTICLE
C: 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3'
D: 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3'
E: HOMEOTIC PROTEIN ULTRABITHORAX
F: HOMEOTIC PROTEIN EXTRADENTICLE
G: 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3'
H: 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)55,2548
Polymers55,2548
Non-polymers00
Water2,882160
1
A: HOMEOTIC PROTEIN ULTRABITHORAX
B: HOMEOTIC PROTEIN EXTRADENTICLE
C: 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3'
D: 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)27,6274
Polymers27,6274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HOMEOTIC PROTEIN ULTRABITHORAX
F: HOMEOTIC PROTEIN EXTRADENTICLE
G: 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3'
H: 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)27,6274
Polymers27,6274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.670, 95.920, 69.820
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HOMEOTIC PROTEIN ULTRABITHORAX


Mass: 9591.063 Da / Num. of mol.: 2 / Fragment: HOMEODOMAIN AND UBDA, RESIDUES 292-367 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P83949
#2: Protein HOMEOTIC PROTEIN EXTRADENTICLE


Mass: 8857.946 Da / Num. of mol.: 2 / 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*C)-3'


Mass: 4537.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: UBX-EXD CONSENSUS BINDING SITE / 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*G)-3'


Mass: 4640.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: UBX-EXD CONSENSUS BINDING SITE / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST G FROM FUSION TAG AFTER CLEAVAGE

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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: 2.56 Å3/Da / Density % sol: 57.16 % / Description: NONE
Crystal growpH: 4.5
Details: 0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.55→38.55 Å / Num. obs: 18169 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 57.22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.6
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8I

1b8i


Resolution: 2.55→38.55 Å / Cor.coef. Fo:Fc: 0.9291 / Cor.coef. Fo:Fc free: 0.8915 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 923 5.08 %RANDOM
Rwork0.1874 ---
obs0.1901 18169 --
Displacement parametersBiso mean: 39.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.3945 Å20 Å24.1016 Å2
2--4.7563 Å20 Å2
3----5.1508 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.55→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 1218 0 160 3652
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013680HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.255195HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1583SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes385HARMONIC5
X-RAY DIFFRACTIONt_it3680HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion19.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion471SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3688SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.71 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3113 172 5.85 %
Rwork0.1991 2769 -
all0.2058 2941 -
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)
15.64550.73650.42091.8986-0.1863.5660.1284-0.2055-0.1441-0.0111-0.144-0.03790.09830.12670.0157-0.1390.01930.0129-0.1135-0.0043-0.059623.82123.092111.4947
21.36271.2351.82014.04991.21987.09120.0253-0.1725-0.00990.6078-0.18690.03140.4363-0.48820.1616-0.0916-0.0454-0.0627-0.0925-0.0018-0.10559.5764-15.3594-8.6482
33.91070.54161.79814.76910.67889.84080.10880.02430.01080.0633-0.1643-0.21280.19220.24970.0555-0.14240.0141-0.0241-0.20740.0205-0.149121.8112-1.52020.0287
45.8234-0.16363.34025.0478-0.6688.39040.37880.1607-0.2851-0.3039-0.338-0.28780.73210.361-0.0408-0.02730.06170.0377-0.2838-0.0452-0.207720.9814-7.6985-0.5875
58.17271.97071.44172.50830.13724.36780.1295-0.0459-0.26540.07340.14180.23850.2139-0.1376-0.2713-0.15450.0070.0576-0.17620.07540.00773.1897-21.8297-24.4347
61.26951.2745-1.33673.9398-1.80644.30140.0398-0.0808-0.1384-0.1485-0.2128-0.22530.10940.54850.173-0.15550.0430.02470.00280.0342-0.006920.9143-4.434-42.0984
73.8084-0.1086-2.00526.7844-2.45355.5994-0.00130.0765-0.5812-0.38-0.10670.03850.3246-0.15560.108-0.2126-0.046-0.0329-0.1867-0.04380.02816.4602-18.0648-35.4671
85.14770.9495-1.70416.8617-2.71583.56230.02940.3157-0.1199-0.4927-0.06810.29020.2226-0.26320.0388-0.11250.0582-0.018-0.18270.0604-0.09927.3662-12.1345-36.4467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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