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- PDB-2ly4: HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transact... -

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Basic information

Entry
Database: PDB / ID: 2ly4
TitleHMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail
Components
  • Cellular tumor antigen p53
  • High mobility group protein B1
KeywordsNUCLEAR PROTEIN/ANTITUMOUR PROTEIN / HMG / p53 / TAD / NUCLEAR PROTEIN-ANTITUMOUR PROTEIN complex
Function / homology
Function and homology information


regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / neutrophil clearance / positive regulation of glycogen catabolic process / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / RAGE receptor binding / positive regulation of interleukin-1 production / eye development / Regulation of TLR by endogenous ligand / bubble DNA binding / V(D)J recombination / alphav-beta3 integrin-HMGB1 complex / myeloid cell differentiation / myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / inflammatory response to antigenic stimulus / regulation of nucleotide-excision repair / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / positive regulation of monocyte chemotactic protein-1 production / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interleukin-7 / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / endothelial cell proliferation / positive regulation of chemokine (C-X-C motif) ligand 2 production / glycogen catabolic process / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / apoptotic cell clearance / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / supercoiled DNA binding / glucose catabolic process to lactate via pyruvate / positive regulation of vascular endothelial cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / dendritic cell chemotaxis / DNA binding, bending / IRAK4 deficiency (TLR2/4) / regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of DNA binding / histone deacetylase regulator activity / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / positive regulation of wound healing / phosphatidylserine binding / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication
Similarity search - Function
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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif ...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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / high mobility group / High mobility group box domain / High mobility group box domain superfamily / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellular tumor antigen p53 / High mobility group protein B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsRowell, J.P. / Simpson, K.L. / Stott, K. / Watson, M. / Thomas, J.O.
CitationJournal: Structure / Year: 2012
Title: HMGB1-Facilitated p53 DNA Binding Occurs via HMG-Box/p53 Transactivation Domain Interaction, Regulated by the Acidic Tail.
Authors: Rowell, J.P. / Simpson, K.L. / Stott, K. / Watson, M. / Thomas, J.O.
History
DepositionSep 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: High mobility group protein B1
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)19,6862
Polymers19,6862
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 9705.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMG1, HMGB1 / Plasmid: pT7-7 HMG1-A / Production host: Escherichia coli (E. coli) / References: UniProt: P09429
#2: Protein Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 9981.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P53, TP53 / Plasmid: pET16b-p53(1-93) / Production host: Escherichia coli (E. coli) / References: UniProt: P04637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-13C NOESY
1413D 1H-13C NOESY, X-filtered
1513D HNCA
1613D HN(CO)CA
1713D HBHA(CO)NH
1813D HNCO
1913D C(CO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N TOCSY
11213D 1H-15N NOESY

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Sample preparation

DetailsContents: 10 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMsodium phosphate-11
1 mMEDTA-21
1 mMDTT-31
0.5 mMPMSF-41
Sample conditionsIonic strength: 0.01 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
AzaraBoucherprocessing
ARIACCPNstructure solution
AnalysisCCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / 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: 10

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