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- PDB-2b3g: p53N (fragment 33-60) bound to RPA70N -

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Basic information

Entry
Database: PDB / ID: 2b3g
Titlep53N (fragment 33-60) bound to RPA70N
Components
  • Cellular tumor antigen p53
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsREPLICATION / OB-fold / ssDNA mimicry
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / lateral element / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / negative regulation of helicase activity / signal transduction by p53 class mediator ...protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / lateral element / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of fibroblast apoptotic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / : / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / germ cell nucleus / regulation of tissue remodeling / ATP-dependent DNA/DNA annealing activity / thymocyte apoptotic process / oligodendrocyte apoptotic process / oxidative stress-induced premature senescence / positive regulation of mitochondrial membrane permeability / positive regulation of thymocyte apoptotic process / bone marrow development / cellular response to actinomycin D / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / circadian behavior / T cell lineage commitment / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / B cell lineage commitment / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / chromatin-protein adaptor activity / Removal of the Flap Intermediate from the C-strand / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Association with Co-factors / ER overload response / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / neuroblast proliferation / cardiac septum morphogenesis / necroptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / HDR through Single Strand Annealing (SSA) / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / hematopoietic stem cell differentiation / negative regulation of mitophagy / Zygotic genome activation (ZGA) / somitogenesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / rRNA transcription / negative regulation of reactive oxygen species metabolic process / Impaired BRCA2 binding to RAD51 / replicative senescence / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TFIID-class transcription factor complex binding / Transcriptional Regulation by VENTX / cellular response to UV-C / hematopoietic progenitor cell differentiation / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / PCNA-Dependent Long Patch Base Excision Repair / embryonic organ development / chromosome organization / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / response to X-ray / positive regulation of execution phase of apoptosis / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / Presynaptic phase of homologous DNA pairing and strand exchange / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest
Similarity search - Function
Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBochkareva, E. / Kaustov, L. / Ayed, A. / Yi, G.S. / Lu, Y. / Pineda-Lucena, A. / Liao, J.C. / Okorokov, A.L. / Milner, J. / Arrowsmith, C.H. / Bochkarev, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A.
Authors: Bochkareva, E. / Kaustov, L. / Ayed, A. / Yi, G.S. / Lu, Y. / Pineda-Lucena, A. / Liao, J.C. / Okorokov, A.L. / Milner, J. / Arrowsmith, C.H. / Bochkarev, A.
History
DepositionSep 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)16,6022
Polymers16,6022
Non-polymers00
Water2,324129
1
A: Replication protein A 70 kDa DNA-binding subunit
B: Cellular tumor antigen p53

A: Replication protein A 70 kDa DNA-binding subunit
B: Cellular tumor antigen p53

A: Replication protein A 70 kDa DNA-binding subunit
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)49,8066
Polymers49,8066
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)49.460, 50.380, 52.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A / RF-A / Replication factor-A protein 1 / Single-stranded DNA-binding protein


Mass: 13469.647 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 1-120)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Plasmid: PET15B-RPA70N-p53N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27694
#2: Protein/peptide Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 3132.386 Da / Num. of mol.: 1 / Fragment: residues 33-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: PET15B-RPA70N-p53N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / pH: 7.9
Details: Na3 Citrate, Hepes, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.90

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2004 / Details: RIGAKU/MSC CONFOCAL MULTILYER OPTICS
RadiationMonochromator: RIGAKU/MSC CONFOCAL MULTILYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 17517 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.046 / Net I/σ(I): 32.5
Reflection shellResolution: 1.6→1.66 Å / % possible all: 83.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B29

2b29


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.278 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 893 5.1 %RANDOM
Rwork0.204 ---
obs0.205 16581 98.2 %-
all-16581 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.91 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 129 1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221093
X-RAY DIFFRACTIONr_bond_other_d0.0020.021027
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9981481
X-RAY DIFFRACTIONr_angle_other_deg0.91732406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021181
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02180
X-RAY DIFFRACTIONr_nbd_refined0.250.2233
X-RAY DIFFRACTIONr_nbd_other0.2570.21231
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.5695
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24821132
X-RAY DIFFRACTIONr_scbond_it3.173398
X-RAY DIFFRACTIONr_scangle_it5.5084.5349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 51 -
Rwork0.466 970 -
obs--79.95 %

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