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- PDB-2xhs: Crystal structure of the ligand binding domain of Fushi tarazu fa... -

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Basic information

Entry
Database: PDB / ID: 2xhs
TitleCrystal structure of the ligand binding domain of Fushi tarazu factor 1 of Drosophila melanogaster.
Components
  • NUCLEAR HORMONE RECEPTOR FTZ-F1
  • SEGMENTATION PROTEIN FUSHI TARAZU
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


pupation / instar larval or pupal development / juvenile hormone mediated signaling pathway / periodic partitioning by pair rule gene / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to ecdysone / pupariation / gonadal mesoderm development / imaginal disc-derived leg morphogenesis ...pupation / instar larval or pupal development / juvenile hormone mediated signaling pathway / periodic partitioning by pair rule gene / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / response to ecdysone / pupariation / gonadal mesoderm development / imaginal disc-derived leg morphogenesis / regulation of development, heterochronic / mushroom body development / segmentation / metamorphosis / tissue development / germ cell migration / cell fate specification / anterior/posterior pattern specification / dendrite morphogenesis / neuron remodeling / lipid homeostasis / hormone-mediated signaling pathway / central nervous system development / RNA polymerase II transcription regulator complex / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Fushi tarazu, N-terminal / Fushi tarazu (FTZ), N-terminal region / : / Nuclear hormone receptor family 5 / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Fushi tarazu, N-terminal / Fushi tarazu (FTZ), N-terminal region / : / Nuclear hormone receptor family 5 / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Retinoid X Receptor / Retinoid X Receptor / Homeobox-like domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Segmentation protein fushi tarazu / Nuclear hormone receptor FTZ-F1
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsYoo, J.H. / Cho, H.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Fushi Tarazu Factor 1 Ligand Binding Domain/Fushi Tarazu Peptide Complex Identifies New Class of Nuclear Receptors.
Authors: Yoo, J. / Ko, S. / Kim, H. / Sampson, H. / Yun, J.H. / Choe, K.M. / Chang, I. / Arrowsmith, C.H. / Krause, H.M. / Cho, H.S. / Lee, W.
History
DepositionJun 21, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionJul 20, 2011ID: 2IZ2
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.3Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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

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Assembly

Deposited unit
A: NUCLEAR HORMONE RECEPTOR FTZ-F1
B: SEGMENTATION PROTEIN FUSHI TARAZU


Theoretical massNumber of molelcules
Total (without water)29,7932
Polymers29,7932
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6.7 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.931, 97.931, 123.466
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NUCLEAR HORMONE RECEPTOR FTZ-F1 / FTZ-F1 ALPHA / NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 3 / NR5A3


Mass: 28804.346 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 791-1027
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P33244
#2: Protein/peptide SEGMENTATION PROTEIN FUSHI TARAZU


Mass: 989.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 107-115 / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P02835
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.3M SODIUM CITRATE TRI-BASIC, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97939
DetectorType: BRUKER / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 25725 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.08
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.8→18.6 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.591 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITION. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 875 5.1 %RANDOM
Rwork0.217 ---
obs0.219 16400 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 0 3 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.962795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2765247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37225104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.76815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.291511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211548
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.2970
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3350.21453
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0991.51247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23322011
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1483823
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2384.5784
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 62 -
Rwork0.37 1173 -
obs--100 %

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