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- PDB-1axc: HUMAN PCNA -

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Basic information

Entry
Database: PDB / ID: 1axc
TitleHUMAN PCNA
Components
  • P21/WAF1
  • PCNAProliferating cell nuclear antigen
KeywordsCOMPLEX (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 / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity ...cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / intestinal epithelial cell maturation / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / cellular response to extracellular stimulus / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / tissue regeneration / regulation of cell cycle G1/S phase transition / Transcriptional regulation by RUNX2 / Processive synthesis on the C-strand of the telomere / negative regulation of phosphorylation / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of DNA biosynthetic process / response to arsenic-containing substance / replisome / oncogene-induced cell senescence / positive regulation of programmed cell death / Transcriptional activation of cell cycle inhibitor p21 / RUNX3 regulates CDKN1A transcription / AKT phosphorylates targets in the cytosol / response to L-glutamate / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone acetyltransferase binding / leading strand elongation / stress-induced premature senescence / DNA polymerase processivity factor activity / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / response to corticosterone / replication fork processing / cellular response to UV-B / G1/S-Specific Transcription / molecular function inhibitor activity / response to dexamethasone / protein kinase inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / nuclear replication fork / p53-Dependent G1 DNA Damage Response / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / SUMOylation of DNA replication proteins / estrous cycle / keratinocyte proliferation / PCNA-Dependent Long Patch Base Excision Repair / response to X-ray / replicative senescence / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / response to hyperoxia / translesion synthesis / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of protein kinase activity / positive regulation of DNA replication / animal organ regeneration / response to cadmium ion / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / DNA polymerase binding / Cyclin E associated events during G1/S transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of B cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / base-excision repair, gap-filling / keratinocyte differentiation / response to organonitrogen compound / positive regulation of DNA repair / epithelial cell differentiation / cellular response to amino acid starvation / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / cyclin binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / protein sequestering activity / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest
Similarity search - Function
Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. ...Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Cyclin-dependent kinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGulbis, J.M. / Kuriyan, J.
CitationJournal: 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
DepositionOct 14, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PCNA
B: P21/WAF1
C: PCNA
D: P21/WAF1
E: PCNA
F: P21/WAF1


Theoretical massNumber of molelcules
Total (without water)94,7256
Polymers94,7256
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-40 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.500, 83.500, 233.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PCNA / Proliferating cell nuclear antigen / PROLIFERATING CELL NUCLEAR ANTIGEN


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 P21/WAF1


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Mspermine1drop
2100 mMsodium citrate1reservoir
330 %(v/v)MPD1reservoir
4200 mMsodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorDate: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 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

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.289 -10 %RANDOM
Rwork0.192 ---
obs0.192 22893 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.95 Å20 Å20 Å2
2--9.95 Å20 Å2
3----19.91 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7509 0 0 295 7804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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