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- PDB-1ahd: DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HO... -

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Entry
Database: PDB / ID: 1ahd
TitleDETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX
Components
  • DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
  • Homeotic protein antennapedia
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


specification of segmental identity, thorax / anterior/posterior axis specification / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / 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) / Homeotic protein antennapedia
Similarity search - Component
Biological speciesDrosophila subobscura (fry)
MethodSOLUTION NMR
AuthorsBilleter, M. / Qian, Y.Q. / Otting, G. / Muller, M. / Gehring, W.J. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.
Authors: Billeter, M. / Qian, Y.Q. / Otting, G. / Muller, M. / Gehring, W. / Wuthrich, K.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain
Authors: Qian, Y.Q. / Otting, G. / Billeter, M. / Mueller, M. / Gehring, W.J. / Wuthrich, K.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Determination of the Three-Dimensional Structure of the Antennapedia Homeodomain from Drosophila in Solution by 1H Nuclear Magnetic Resonance Spectroscopy
Authors: Billeter, M. / Qian, Y.-Q. / Otting, G. / Mueller, M. / Gehring, W.J. / Wuthrich, K.
#3: Journal: Embo J. / Year: 1990
Title: Protein-DNA Contacts in the Structure of a Homeodomain-DNA Complex Determined by Nuclear Magnetic Resonance Spectroscopy in Solution
Authors: Otting, G. / Qian, Y.Q. / Billeter, M. / Mueller, M. / Affolter, M. / Gehring, W.J. / Wuthrich, K.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1989
Title: The Structure of the Antennapedia Homeodomain Determined by NMR Spectroscopy in Solution: Comparison with Prokaryotic Repressors
Authors: Qian, Y.-Q. / Billeter, M. / Otting, G. / Mueller, M. / Gehring, W.J. / Wuthrich, K.
History
DepositionApr 2, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 30, 2016Group: Structure summary
Revision 1.4Apr 10, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
B: DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
P: Homeotic protein antennapedia


Theoretical massNumber of molelcules
Total (without water)17,2213
Polymers17,2213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / -
Representative

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Components

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


Mass: 4337.855 Da / Num. of mol.: 1 / Mutation: C39S / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')


Mass: 4221.751 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Homeotic protein antennapedia


Mass: 8661.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila subobscura (fry) / Gene: Antp / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: Q24645

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR ensembleConformers submitted total number: 16

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