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- PDB-1e7j: HMG-D complexed to a bulge DNA -

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Basic information

Entry
Database: PDB / ID: 1e7j
TitleHMG-D complexed to a bulge DNA
Components
  • DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*CP*AP*AP*TP*AP*TP*CP*G)-3')
  • HIGH MOBILITY GROUP PROTEIN DHigh-mobility group
KeywordsPROTEIN/DNA / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / chromatin organization / transcription cis-regulatory region binding / chromatin / DNA binding / nucleus
Similarity search - Function
High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / High mobility group protein D
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / SIMULATED ANNEALING, MINIMIZATION
AuthorsCerdan, R. / Payet, D. / Yang, J.-C. / Travers, A.A. / Neuhaus, D.
Citation
Journal: Protein Sci. / Year: 2001
Title: Hmg-D Complexed to a Bulge DNA: An NMR Model
Authors: Cerdan, R. / Payet, D. / Yang, J.-C. / Travers, A.A. / Neuhaus, D.
#1: Journal: Structure / Year: 1994
Title: The Solution Structure and Dynamics of the DNA-Binding Domain of Hmg-D from Drosophila Melanogaster
Authors: Jones, D.N.M. / Searles, M.A. / Shaw, G.L. / Churchill, M.E.A. / Ner, S.S. / Keeler, J. / Travers, A.A. / Neuhaus, D.
History
DepositionAug 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIGH MOBILITY GROUP PROTEIN D
B: DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*TP*CP*AP*AP*TP*AP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)16,4533
Polymers16,4533
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)10 / 50LOW VALUES OF THE NOE ENERGY TERM AND PROTEIN LOCATED WITHIN MINOR GROOVE OF DNA
RepresentativeModel #1

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Components

#1: Protein HIGH MOBILITY GROUP PROTEIN D / High-mobility group / HMG-D


Mass: 8501.711 Da / Num. of mol.: 1 / Fragment: HMG-D DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET13A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05783
#2: DNA chain DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*C)-3')


Mass: 4288.817 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*GP*CP*TP*CP*AP*AP*TP*AP*TP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
14115N-HSQC
1513D CBCA(CO)NH
1613D 15N NOESY-HSQC
1713D 13C NOESY-HSQC
1813D (H)CCH-TOCSY

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Sample preparation

Sample conditionsIonic strength: LOW / pH: 6.0 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX6002
Bruker AvanceBrukerAvance8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR 3.851, CHARMM24BRUNGER, MACKERELLrefinement
XPLOR3.851structure solution
CHARMM24structure solution
RefinementMethod: SIMULATED ANNEALING, MINIMIZATION / Software ordinal: 1 / Details: REFINEMENT DETAILS WILL BE FOUND IN THE PAPER
NMR ensembleConformer selection criteria: LOW VALUES OF THE NOE ENERGY TERM AND PROTEIN LOCATED WITHIN MINOR GROOVE OF DNA
Conformers calculated total number: 50 / Conformers submitted total number: 10

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