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- PDB-2ezg: SOLUTION STRUCTURE OF A COMPLEX OF THE THIRD DNA BINDING DOMAIN O... -

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Basic information

Entry
Database: PDB / ID: 2ezg
TitleSOLUTION STRUCTURE OF A COMPLEX OF THE THIRD DNA BINDING DOMAIN OF HUMAN HMG-I(Y) BOUND TO DNA DODECAMER CONTAINING THE PRDII SITE OF THE INTERFERON-BETA PROMOTER, NMR, 35 STRUCTURES
Components
  • DNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3')
  • HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-YHigh-mobility group
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN / MINOR GROOVE DNA BINDING / TRANSCRIPTIONAL CO-ACTIVATOR / ARCHITECTURAL FACTOR / COMPLEX (DNA-BINDING PROTEIN-DNA) / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


senescence-associated heterochromatin focus / nucleosome disassembly / nuclear retinoic acid receptor binding / oncogene-induced cell senescence / peroxisome proliferator activated receptor binding / DNA binding, bending / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA unwinding involved in DNA replication ...senescence-associated heterochromatin focus / nucleosome disassembly / nuclear retinoic acid receptor binding / oncogene-induced cell senescence / peroxisome proliferator activated receptor binding / DNA binding, bending / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA unwinding involved in DNA replication / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / minor groove of adenine-thymine-rich DNA binding / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / 5'-deoxyribose-5-phosphate lyase activity / cis-regulatory region sequence-specific DNA binding / nuclear retinoid X receptor binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / nuclear receptor coactivator activity / molecular function activator activity / transcription coregulator binding / transcription coregulator activity / base-excision repair / RNA polymerase II transcription regulator complex / structural constituent of chromatin / transcription regulator complex / transcription coactivator activity / molecular adaptor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / focal adhesion / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
High mobility group protein HMGA / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif
Similarity search - Domain/homology
DNA / DNA (> 10) / High mobility group protein HMG-I/HMG-Y
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Huth, J.R. / Bewley, C. / Gronenborn, A.M.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.
Authors: Huth, J.R. / Bewley, C.A. / Nissen, M.S. / Evans, J.N. / Reeves, R. / Gronenborn, A.M. / Clore, G.M.
History
DepositionJun 4, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,5103
Polymers8,5103
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)35 / 35
Representative

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Components

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


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein/peptide HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-Y / High-mobility group / HIGH MOBILITY GROUP PROTEIN HMG


Mass: 1185.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P17096

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DATA WERE RECORDED ON A 2:1 COMPLEX OF DNA DODECAMER TO HMG-I(Y) 50-91 WHICH CONTAINS THE SECOND AND THIRD DNA DNA BINDING DOMAINS. EACH DNA BINDING DOMAIN BINDS TO 1 MOLECULE OF DNA.

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 306 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5006001
Bruker AMX600BrukerAMX6005002
Bruker DMX600BrukerDMX6007503
Bruker DMX750BrukerDMX7507504

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XPLOR MODIFIEDMODIFIEDstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080 AND (1997) J. MAGN. RESON. 125, 171-177) THE 3D STRUCTURE OF THE COMPLEX OF THE THIRD DNA BINDING DOMAIN OF HMG-I(Y) COMPLEXED TO DNA WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR (A) PROTEIN: 31 SEQUENTIAL (|I-J|=1), 2 MEDIUM RANGE (1 < |I-J| >=5) AND 22 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 17 TORSION ANGLE RESTRAINTS 6 THREE-BOND HN-HA AND 3 THREE_BOND COCO COUPLING CONSTANT RESTRAINTS; 17 (9 CALPHA AND 8 CBETA) 13C SHIFT RESTRAINTS. (B) DNA: 249 INTRARESIDUE, 119 SEQUENTIAL INTRASTRAND AND 33 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 42 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 136 TORSION ANGLE RESTRAINTS (C) 34 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS (D) 4 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES (E) 28 'REPULSIVE' RESTRAINTS THE STRUCTURES IN THIS ENTRY ARE THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES. THE RESTRAINTS REGULARIZED MEAN STRUCTURE IS FOUND IN PDB ENTRY 2EZF. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. RESIDUES 32 - 41 OF THE PROTEIN CORRESPOND TO RESIDUES 79 - 88 OF INTACT HMG-I(Y).
NMR ensembleConformers calculated total number: 35 / Conformers submitted total number: 35

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