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- PDB-1nk3: VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1nk3
TitleVND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3')
  • HOMEOBOX PROTEIN VND
KeywordsDNA BINDING PROTEIN/DNA / HOMEODOMAIN / HOMEOBOX / DNA-BINDING PROTEIN / EMBRYONIC DEVELOPMENT / COMPLEX (HOMEODOMAIN-DNA) / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


neuroblast development / neuroblast fate determination / glial cell development / brain development / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II ...neuroblast development / neuroblast fate determination / glial cell development / brain development / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...: / 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 vnd
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsGruschus, J.M. / Tsao, D.H.H. / Wang, L.-H. / Nirenberg, M. / Ferretti, J.A.
Citation
Journal: Biochemistry / Year: 1997
Title: Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
Authors: Gruschus, J.M. / Tsao, D.H. / Wang, L.H. / Nirenberg, M. / Ferretti, J.A.
#1: Journal: Biochemistry / Year: 1997
Title: Interactions of the Vnd/Nk-2 Homeodomain with DNA by Nuclear Magnetic Resonance Spectroscopy: Basis of Binding Specificity
Authors: Gruschus, J.M. / Tsao, D.H. / Wang, L.H. / Nirenberg, M. / Ferretti, J.A.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: The Three-Dimensional Solution Structure of the Nk-2 Homeodomain from Drosophila
Authors: Tsao, D.H. / Gruschus, J.M. / Wang, L.H. / Nirenberg, M. / Ferretti, J.A.
#3: Journal: Biochemistry / Year: 1994
Title: Elongation of Helix III of the Nk-2 Homeodomain Upon Binding to DNA: A Secondary Structure Study by NMR
Authors: Tsao, D.H. / Gruschus, J.M. / Wang, L.H. / Nirenberg, M. / Ferretti, J.A.
History
DepositionMay 6, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3')
B: DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3')
P: HOMEOBOX PROTEIN VND


Theoretical massNumber of molelcules
Total (without water)19,1713
Polymers19,1713
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)1 / 80LEAST RESTRAINT VIOLATION
Representative

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Components

#1: DNA chain DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3')


Mass: 4960.211 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3')


Mass: 4836.171 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein HOMEOBOX PROTEIN VND / VND/NK-2 HOMEODOMAIN / VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN / HOMEOBOX PROTEIN NK-2


Mass: 9374.741 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: POTENTIAL / Organ: FRUIT / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: P22808

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED 3D NOESY H2O
12113C-EDITED 3D NOESY D2O
13112C-FILTERED 2D NOESY D2O
1411-1 SEMISELECTIVE 2D NOESY H2O
151DEUTERIUM EXCHANGE 15N 2D HMQC H2O
161QUANTITATIVE HN-HALPHA J-COUPLING
NMR detailsText: THIS MODEL IS THE AVERAGE STRUCTURE OF THE ENSEMBLE OF 20 STRUCTURES (1NK2). THE UNSTRUCTURED N-TERMINAL AND C-TERMINAL AMINO ACIDS (P 101-P 107 AND P 171-P 177 IN PDB ENTRY 1NK2) WERE REMOVED ...Text: THIS MODEL IS THE AVERAGE STRUCTURE OF THE ENSEMBLE OF 20 STRUCTURES (1NK2). THE UNSTRUCTURED N-TERMINAL AND C-TERMINAL AMINO ACIDS (P 101-P 107 AND P 171-P 177 IN PDB ENTRY 1NK2) WERE REMOVED PRIOR TO MINIMIZATION OF THE AVERAGE STRUCTURE BY THE MD_SCHE DULE PROGRAM OF INSIGHTII/NMR REFINE, SUBJECT TO ALL EXPERIMENTAL RESTRAINTS FOR THE DNA AND REMAINING PROTEIN RESIDUES. THE REMAINING PROTEIN RESIDUES ARE RENUMBERED STARTING WITH P 100 SO THAT THE RESIDUE NUMBERING FOLLOWS THE STANDARD, CANONICAL NUMBER ING SCHEME FOR HOMEODOMAINS.

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 60mM / pH: 6 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
INSIGHT II 97 AUTHOR : MSIMSIrefinement
NMR REFINEREFINEstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: NMR REFINE/INSIGHT II 97
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 80 / Conformers submitted total number: 1

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