General Information

Database Accession: DI3000004

Name: C-terminal region of p21(WAF1/CIP1) complexed with human PCNA.

PDB ID: 1axc PDB

Experimental method: X-ray (2.60 Å)

Source organism: Homo sapiens

Proof of disorder: Confirmed

Kd: 8.80×10-08 M PubMed

Primary publication of the structure:

Gulbis JM, Kelman Z, Hurwitz J, O'Donnell M, Kuriyan J
Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA.

(1996) Cell 87: 297-306

PMID: 8861913 PubMed

Abstract:

The crystal structure of the human DNA polymerase delta processivity factor PCNA (proliferating cell nuclear antigen) complexed with a 22 residue peptide derived from the C-terminus of the cell-cycle checkpoint protein p21(WAF1/CIP1) has been determined at 2.6 angstrom resolution. p21 binds to PCNA in a 1:1 stoichiometry with an extensive array of interactions that include the formation of a beta sheet with the interdomain connector loop of PCNA. An intact trimeric ring is maintained in the structure of the p21-PCNA complex, with a central hole available for DNA interaction. The ability of p21 to inhibit the action of PCNA is therefore likely to be due to its masking of elements on PCNA that are required for the binding of other components of the polymerase assembly.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

enzyme regulator activity Binds to and modulates the activity of an enzyme. GeneOntology

protein kinase binding Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. GeneOntology

protein complex binding Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules). GeneOntology

Biological process:

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle. GeneOntology

G1/S transition of mitotic cell cycle The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated. GeneOntology

regulation of nucleic acid-templated transcription Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. GeneOntology

regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GeneOntology

regulation of cellular macromolecule biosynthetic process Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process. GeneOntology

epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. GeneOntology

positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GeneOntology

positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GeneOntology

regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. GeneOntology

cellular response to UV Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers. GeneOntology

response to glucocorticoid Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects. GeneOntology

animal organ regeneration The regrowth of a lost or destroyed organ. GeneOntology

response to organonitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. GeneOntology

Cellular component:

nuclear body Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. GeneOntology

PCNA-p21 complex A protein complex that contains the cyclin-dependent protein kinase inhibitor p21WAF1/CIP1 bound to PCNA; formation of the complex inhibits DNA replication. GeneOntology

intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 4 distinct polypeptide molecules

Chains: B, A, C, E

Notes: Chains D and F were removed as chains A, B, C and E represent the biologically relevant interaction.

Chain B

Name: Cyclin-dependent kinase inhibitor 1 Disordered Confirmed

Source organism: Homo sapiens

Length: 18 residues

Sequence:Sequence according to PDB SEQRESRQTSMTDFYHSKRRLIFS

UniProtKB AC: P38936 (positions: 143-160) UniProt Coverage: 11%

UniRef90 AC: UniRef90_P38936 (positions: 143-160) UniRef90

Chain A

Name: Proliferating cell nuclear antigen Ordered component

Source organism: Homo sapiens

Length: 255 residues

Sequence:Sequence according to PDB SEQRESMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI

UniProtKB AC: P12004 (positions: 1-255) UniProt Coverage: 97.7%

UniRef90 AC: UniRef90_P12004 (positions: 1-255) UniRef90

Chain C

Name: Proliferating cell nuclear antigen Ordered component

Source organism: Homo sapiens

Length: 255 residues

Sequence:Sequence according to PDB SEQRESMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI

UniProtKB AC: P12004 (positions: 1-255) UniProt Coverage: 97.7%

UniRef90 AC: UniRef90_P12004 (positions: 1-255) UniRef90

Chain E

Name: Proliferating cell nuclear antigen Ordered component

Source organism: Homo sapiens

Length: 255 residues

Sequence:Sequence according to PDB SEQRESMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI

UniProtKB AC: P12004 (positions: 1-255) UniProt Coverage: 97.7%

UniRef90 AC: UniRef90_P12004 (positions: 1-255) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Chain B: Disordered Confirmed

The 1-164 region described in DisProt entry DP00016 and in IDEAL entry IID00043 cover 100% of the sequence present in the structure. The protein region involved in the interaction contains four known functional linear motifs (DEG_CRL4_CDT2_1, DOC_CYCLIN_1, LIG_PCNA_PIPBox_1, TRG_NLS_Bipartite_1) and a known modification site (MOD_PKB_1).

Chain A: Ordered component

PCNA forms an ordered homotrimeric ring-shaped complex which encircles duplex DNA, providing a DNA-bound platform for binding substrate proteins (PMID: 8001157). A solved structure of the PCNA homotrimer without bound ligands is represented by PDB ID 1w60.

Chain C: Ordered component

PCNA forms an ordered homotrimeric ring-shaped complex which encircles duplex DNA, providing a DNA-bound platform for binding substrate proteins (PMID: 8001157). A solved structure of the PCNA homotrimer without bound ligands is represented by PDB ID 1w60.

Chain E: Ordered component

PCNA forms an ordered homotrimeric ring-shaped complex which encircles duplex DNA, providing a DNA-bound platform for binding substrate proteins (PMID: 8001157). A solved structure of the PCNA homotrimer without bound ligands is represented by PDB ID 1w60.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There are 2 related structures in the Protein Data Bank:


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