+Open data
-Basic information
Entry | Database: PDB / ID: 1axc | ||||||
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Title | HUMAN PCNA | ||||||
Components |
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Keywords | COMPLEX (DNA-BINDING PROTEIN/DNA) / DNA / REPLICATION / PROCESSIVITY / ONCOGENE / WAF1 / CIP1 / COMPLEX (DNA-BINDING PROTEIN-DNA) / COMPLEX (DNA-BINDING PROTEIN-DNA) complex | ||||||
Function / homology | Function and homology information cyclin-dependent protein kinase activating kinase activity / 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 / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / intestinal epithelial cell maturation / mitotic telomere maintenance via semi-conservative replication ...cyclin-dependent protein kinase activating kinase activity / 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 / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / intestinal epithelial cell maturation / mitotic telomere maintenance via semi-conservative replication / : / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / regulation of cell cycle G1/S phase transition / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / tissue regeneration / Transcriptional regulation by RUNX2 / Processive synthesis on the lagging strand / PCNA complex / negative regulation of phosphorylation / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / cyclin-dependent protein serine/threonine kinase inhibitor activity / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / negative regulation of DNA biosynthetic process / Removal of the Flap Intermediate from the C-strand / response to arsenic-containing substance / replisome / 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 / response to L-glutamate / stress-induced premature senescence / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone acetyltransferase binding / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / response to corticosterone / cellular response to UV-B / molecular function inhibitor activity / DNA polymerase processivity factor activity / G1/S-Specific Transcription / STAT5 activation downstream of FLT3 ITD mutants / leading strand elongation / protein kinase inhibitor activity / response to dexamethasone / replication fork processing / p53-Dependent G1 DNA Damage Response / nuclear replication fork / 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 / SUMOylation of DNA replication proteins / keratinocyte proliferation / response to X-ray / replicative senescence / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of protein kinase activity / response to hyperoxia / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / mismatch repair / translesion synthesis / Cyclin E associated events during G1/S transition / response to cadmium ion / DNA polymerase binding / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of B cell proliferation / keratinocyte differentiation / : / epithelial cell differentiation / protein sequestering activity / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of DNA repair / cellular response to amino acid starvation / Translesion synthesis by REV1 / intrinsic apoptotic signaling pathway / Translesion synthesis by POLK / cyclin binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of protein phosphorylation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gulbis, J.M. / Kuriyan, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Authors: Gulbis, J.M. / Kelman, Z. / Hurwitz, J. / O'Donnell, M. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1axc.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1axc.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 1axc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1axc_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 1axc_full_validation.pdf.gz | 472.3 KB | Display | |
Data in XML | 1axc_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 1axc_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axc ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28795.752 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P12004 #2: Protein/peptide | Mass: 2779.233 Da / Num. of mol.: 3 / Fragment: 22 C TERMINAL RESIDUES (139 - 160) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P38936 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 |
Detector | Date: Oct 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. obs: 33552 / % possible obs: 96 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.073 |
Reflection | *PLUS Num. measured all: 130418 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.278 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: YEAST PCNA Resolution: 2.6→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |