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- PDB-2zvw: Crystal structure of Proliferating cell nuclear antigen 2 and Sho... -
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Basic information
Entry | Database: PDB / ID: 2zvw | ||||||
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Title | Crystal structure of Proliferating cell nuclear antigen 2 and Short peptide from human P21 | ||||||
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![]() | DNA BINDING PROTEIN / protein-peptide complex / DNA replication / DNA-binding / Nucleus | ||||||
Function / homology | ![]() cyclin-dependent protein kinase activating kinase activity / cellular response to cell-matrix adhesion / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / PCNA-p21 complex / intestinal epithelial cell maturation / regulation of cell cycle G1/S phase transition / tissue regeneration ...cyclin-dependent protein kinase activating kinase activity / cellular response to cell-matrix adhesion / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / PCNA-p21 complex / intestinal epithelial cell maturation / regulation of cell cycle G1/S phase transition / tissue regeneration / Transcriptional regulation by RUNX2 / PCNA complex / negative regulation of phosphorylation / negative regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to arsenic-containing substance / positive regulation of programmed cell death / oncogene-induced cell senescence / Transcriptional activation of cell cycle inhibitor p21 / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / stress-induced premature senescence / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / response to corticosterone / cellular response to UV-B / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular function inhibitor activity / DNA polymerase processivity factor activity / STAT5 activation downstream of FLT3 ITD mutants / protein kinase inhibitor activity / leading strand elongation / p53-Dependent G1 DNA Damage Response / regulation of DNA replication / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / keratinocyte proliferation / response to X-ray / replicative senescence / positive regulation of protein kinase activity / response to hyperoxia / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / animal organ regeneration / mismatch repair / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / error-prone translesion synthesis / translesion synthesis / Cyclin E associated events during G1/S transition / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of B cell proliferation / keratinocyte differentiation / : / regulation of G2/M transition of mitotic cell cycle / protein sequestering activity / Signaling by FLT3 fusion proteins / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to amino acid starvation / intrinsic apoptotic signaling pathway / cyclin binding / negative regulation of protein phosphorylation / positive regulation of DNA replication / negative regulation of protein binding / molecular function activator activity / cellular response to ionizing radiation / wound healing / DNA Damage/Telomere Stress Induced Senescence / negative regulation of cell growth / response to toxic substance / cellular response to gamma radiation / SCF(Skp2)-mediated degradation of p27/p21 / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / protein import into nucleus / The role of GTSE1 in G2/M progression after G2 checkpoint / Cyclin D associated events in G1 / positive regulation of reactive oxygen species metabolic process / KEAP1-NFE2L2 pathway / cellular senescence / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / Neddylation / heart development / cellular response to heat / fibroblast proliferation / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / in utero embryonic development / Ras protein signal transduction / nuclear body / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Strzalka, W. / Oyama, T. / Tori, K. / Morikawa, K. | ||||||
![]() | ![]() Title: Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment Authors: Strzalka, W. / Oyama, T. / Tori, K. / Morikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 408.7 KB | Display | ![]() |
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PDB format | ![]() | 336.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zvvC ![]() 1axcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30334.625 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2779.233 Da / Num. of mol.: 8 / Fragment: UNP residues 139-160 / Source method: obtained synthetically / Details: A synthetic fragment 139-160 of the human p21/WAF1 / References: UniProt: P38936 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM citric acid, 1.8M ammonium salfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 13, 2008 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 129598 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 45.1 Å2 / Rsym value: 0.047 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.184 / Num. unique all: 129598 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AXC Resolution: 2.5→36.69 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 211911.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.2552 Å2 / ksol: 0.353001 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→36.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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