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- PDB-2gzk: Structure of a complex of tandem HMG boxes and DNA -

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Basic information

Entry
Database: PDB / ID: 2gzk
TitleStructure of a complex of tandem HMG boxes and DNA
Components
  • 5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*C)-3'
  • 5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP*C)-3'
  • Sex-determining region on Y / HMGB1
KeywordsDNA/STRUCTURAL PROTEIN / PROTEIN-DNA COMPLEX / HMG BOX / amphoterin / DNA-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


tumor necrosis factor production => GO:0032640 / chromatin organization => GO:0006325 / male-specific defense response to bacterium / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / DNA-binding transcription factor binding => GO:0140297 / plasmacytoid dendritic cell activation / regulation of restriction endodeoxyribonuclease activity ...tumor necrosis factor production => GO:0032640 / chromatin organization => GO:0006325 / male-specific defense response to bacterium / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / DNA-binding transcription factor binding => GO:0140297 / plasmacytoid dendritic cell activation / regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / : / regulation of T cell mediated immune response to tumor cell / : / heterochromatin formation => GO:0031507 / positive regulation of mismatch repair / positive regulation of toll-like receptor 2 signaling pathway / negative regulation of apoptotic cell clearance / positive regulation of myeloid cell differentiation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / positive regulation of macrophage inflammatory protein 1 alpha production / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / C-X-C chemokine binding / positive regulation of male gonad development / bent DNA binding / positive regulation of glycogen catabolic process / Transcriptional regulation of testis differentiation / glycolipid binding / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / response to xenobiotic stimulus => GO:0009410 / endothelial cell chemotaxis / sex differentiation / positive regulation of DNA ligation / developmental process / chromatin => GO:0000785 / eye development / positive regulation of interleukin-1 production / RAGE receptor binding / induction of positive chemotaxis / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / male sex determination / V(D)J recombination / regulation of nucleotide-excision repair / macrophage activation involved in immune response / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / inflammatory response to antigenic stimulus / regulation of signaling receptor activity / supercoiled DNA binding / cellular response to interleukin-7 / endothelial cell proliferation / positive regulation of monocyte chemotaxis / apoptotic cell clearance / myoblast proliferation / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / phosphatidylserine binding / positive regulation of wound healing / protein kinase activator activity / negative regulation of DNA replication / positive regulation of activated T cell proliferation / positive regulation of sprouting angiogenesis / response to type II interferon / positive regulation of smooth muscle cell migration / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / transcription factor binding / negative regulation of type II interferon production / endoplasmic reticulum-Golgi intermediate compartment / anatomical structure morphogenesis / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / positive regulation of myoblast differentiation / cellular response to interleukin-1 / response to glucose / DNA polymerase binding / positive regulation of autophagy / four-way junction DNA binding / condensed chromosome / response to glucocorticoid / transcription repressor complex / positive regulation of interferon-beta production / activation of innate immune response / positive regulation of interleukin-12 production / positive regulation of mitotic cell cycle / cell chemotaxis / positive regulation of interleukin-1 beta production / cytokine activity
Similarity search - Function
Transcription factor SRY / HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...Transcription factor SRY / HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / 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) / Sex-determining region Y protein / High mobility group protein B1 / Sex-determining region Y protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus rattus (black rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsStott, K. / Tang, G.S. / Lee, K.B. / Thomas, J.O.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of a Complex of Tandem HMG Boxes and DNA.
Authors: Stott, K. / Tang, G.S. / Lee, K.B. / Thomas, J.O.
History
DepositionMay 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 999SEQUENCE The protein is a chimeric protein, a hybrid, made from the HMG-box domain from human SRY, ...SEQUENCE The protein is a chimeric protein, a hybrid, made from the HMG-box domain from human SRY, comprising residues 56-130 followed by residues 82-165 of rat HMGB1

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP*C)-3'
C: 5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*C)-3'
A: Sex-determining region on Y / HMGB1


Theoretical massNumber of molelcules
Total (without water)28,7833
Polymers28,7833
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)1 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4931.230 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*C)-3'


Mass: 4864.163 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Sex-determining region on Y / HMGB1


Mass: 18988.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Rattus rattus / Genus: Homo, Rattus / Species: , / Strain: , / Production host: Escherichia coli (E. coli)
References: UniProt: Q6J4I5, UniProt: Q548R9, UniProt: Q05066*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HSQC
1213D HN(CO)CA
131HNCA-J
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D (H)CC(CO)NH-TOCSY
1813D TOCSY-15N-HSQC
1913D NOESY-15N-HSQC
11013D (H)CCH-TOCSY
11113D NOESY-13C-HSQC
1121HNHA
11312D TOCSY
1141DQF-COSY
11512D NOESY
1161[F1]-13C/15N-filtered TOCSY [F1]-13C/15N-filtered TOCSY
11712D [F1]-13C/15N-filtered DQF COSY
11812D [F1]-13C/15N-filtered NOESY
11913D [F1]-13C/15N-filtered NOESY-13C-HSQC
12012D [F1,F2]-13C/15N-filtered NOESY

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Sample preparation

DetailsContents: 1mM SRY.B U-15N,13C, 1mM 16-mer DNA, 10mM phosphate buffer, pH 6.8, 1mM EDTA, 2mM DTT U-2H, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM phosphate buffer / pH: 6.8 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.7Brukercollection
Azara2.7Boucher, W.processing
Analysis1Boucher, W. and Stevens, T.data analysis
CNS1.1Brunger, A.structure solution
CNS1.1Brunger, A.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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