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- PDB-1lfu: NMR Solution Structure of the Extended PBX Homeodomain Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1lfu
TitleNMR Solution Structure of the Extended PBX Homeodomain Bound to DNA
Components
  • 5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3'
  • 5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3'
  • homeobox protein PBX1
KeywordsTRANSCRIPTION / protein-dna complex
Function / homology
Function and homology information


urogenital system development / natural killer cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / eye development / steroid biosynthetic process / embryonic limb morphogenesis / embryonic hemopoiesis / anterior/posterior pattern specification ...urogenital system development / natural killer cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / eye development / steroid biosynthetic process / embryonic limb morphogenesis / embryonic hemopoiesis / anterior/posterior pattern specification / branching involved in ureteric bud morphogenesis / adrenal gland development / positive regulation of stem cell proliferation / negative regulation of neuron differentiation / regulation of ossification / neuron development / embryonic organ development / spleen development / positive regulation of G2/M transition of mitotic cell cycle / transcription corepressor binding / thymus development / stem cell proliferation / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / brain development / RNA polymerase II transcription regulator complex / G2/M transition of mitotic cell cycle / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox KN domain / Homeobox KN domain / 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) / Pre-B-cell leukemia transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / dynamical annealing
AuthorsSprules, T. / Green, N. / Featherstone, M. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Lock and Key Binding of the HOX YPWM Peptide to the PBX Homeodomain
Authors: Sprules, T. / Green, N. / Featherstone, M. / Gehring, K.
History
DepositionApr 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 27, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3'
B: 5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3'
P: homeobox protein PBX1


Theoretical massNumber of molelcules
Total (without water)18,1403
Polymers18,1403
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest energy with acceptable geometry
RepresentativeModel #1lowest energy

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Components

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


Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3'


Mass: 4305.804 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein homeobox protein PBX1 / / PBX / PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1


Mass: 9577.833 Da / Num. of mol.: 1 / Fragment: homeodomain AND conserved C-terminus / Mutation: C42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PBX1 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P41778

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
3333D 13C-separated NOESY
4442D NOESY
555t1-1H coupled 15N HSQC
666t1-1H coupled 13C HSQC, 13C HMQC
171t1-1H coupled 15N HSQC
484t1-1H coupled 13C HSQC, 13C HMQC
39313C filtered 2D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM U-15N PBX:DNA; 20 mM phophate buffer90% H2O/10% D2O
21 mM U-15N,13C PBX:DNA; 20 mM phosphate buffer90% H2O/10% D2O
31.9 mM U-15N,13C PBX:DNA; 20 mM phosphate buffer100% D2O
41.4 mM PBX:DNA; 20 mM phosphate buffer100% D2O
52.5 mM PBX:DNA; 5% q=3.0 DMPC:DHPC 20 mM phosphate buffer100% D2O
61 mM U-15N PBX:DNA; 5% q=3.0 DMPC:DHPC; 20 mM sodium phosphate90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 ambient 303 K
27.0 ambient 303 K
37.0 ambient 303 K
47.0 ambient 303 K
56.6 ambient 310 K
66.6 ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1proprietary softwarecollection
VNMR6.1Bproprietary softwarecollection
Gifa4.3Pons, J. L., Malliavin, T. E., and Delsuc, M. A.processing
XEASY1.3.13Bartels, C., Xia, T.-H., Billeter, M., Guntert, P., and Wuthrich K.data analysis
ARIA0.5Nigles, M., Macias, M. J., O'Donoghue, S. I., and Oschkinat, H.data analysis
CNS0.9, 1.1Brunger, A. T., et al.refinement
RefinementMethod: dynamical annealing / Software ordinal: 1
Details: Structures based on a total of 2747 restraints: 2508 NOE-derived distance restraints, 84 hydrogen bonds, 68 dihedral angle and J-coupling restraints and 87 residual dipolar couplings.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy with acceptable geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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