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- PDB-6cej: Solution structure of a 14mer fragment of the p21 protein -

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Basic information

Entry
Database: PDB / ID: 6cej
TitleSolution structure of a 14mer fragment of the p21 protein
ComponentsCyclin-dependent kinase inhibitor 1
KeywordsCELL CYCLE / PIP-box motif / p21 / PCNA
Function / homology
Function and homology information


negative regulation of cardiac muscle tissue regeneration / negative regulation of DNA biosynthetic process / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / cellular response to cell-matrix adhesion / import into nucleus / regulation of cell cycle G1/S phase transition / PCNA-p21 complex / Transcriptional regulation by RUNX2 / tissue regeneration ...negative regulation of cardiac muscle tissue regeneration / negative regulation of DNA biosynthetic process / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / cellular response to cell-matrix adhesion / import into nucleus / regulation of cell cycle G1/S phase transition / PCNA-p21 complex / Transcriptional regulation by RUNX2 / tissue regeneration / cyclin-dependent protein serine/threonine kinase inhibitor activity / oncogene-induced cell senescence / Transcriptional activation of cell cycle inhibitor p21 / positive regulation of programmed cell death / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / stress-induced premature senescence / molecular function inhibitor activity / cellular response to UV-B / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of protein kinase activity / p53-Dependent G1 DNA Damage Response / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / protein kinase inhibitor activity / keratinocyte proliferation / replicative senescence / negative regulation of vascular associated smooth muscle cell proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / keratinocyte differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin E associated events during G1/S transition / regulation of G2/M transition of mitotic cell cycle / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of G1/S transition of mitotic cell cycle / positive regulation of B cell proliferation / mitotic G1 DNA damage checkpoint signaling / Signaling by FLT3 fusion proteins / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of DNA replication / molecular function activator activity / cellular response to amino acid starvation / protein serine/threonine kinase binding / cellular response to ionizing radiation / DNA damage response, signal transduction by p53 class mediator / wound healing / protein sequestering activity / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / negative regulation of cell growth / protein import into nucleus / DNA Damage/Telomere Stress Induced Senescence / positive regulation of fibroblast proliferation / positive regulation of reactive oxygen species metabolic process / cellular senescence / Transcriptional regulation of granulopoiesis / SCF(Skp2)-mediated degradation of p27/p21 / Cyclin D associated events in G1 / The role of GTSE1 in G2/M progression after G2 checkpoint / Signaling by ALK fusions and activated point mutants / KEAP1-NFE2L2 pathway / heart development / in utero embryonic development / Neddylation / fibroblast proliferation / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / Ras protein signal transduction / regulation of cell cycle / nuclear body / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / DNA damage response / protein kinase binding / nucleolus / protein-containing complex binding / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor
Similarity search - Domain/homology
Cyclin-dependent kinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWegener, K.L.
CitationJournal: Chemistry / Year: 2018
Title: Rational Design of a 310-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp.
Authors: Wegener, K.L. / McGrath, A.E. / Dixon, N.E. / Oakley, A.J. / Scanlon, D.B. / Abell, A.D. / Bruning, J.B.
History
DepositionFeb 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)1,7881
Polymers1,7881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2230 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cyclin-dependent kinase inhibitor 1 / CDK-interacting protein 1 / Melanoma differentiation-associated protein 6 / MDA-6 / p21


Mass: 1788.020 Da / Num. of mol.: 1 / Fragment: UNP residues 139-152 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P38936

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D COSY
141isotropic11D 1H

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Sample preparation

DetailsType: solution
Contents: 5 mM NA- p21-14mer, 0.1 mM NA- DSS, 90% H2O/10% D2O
Label: p21 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMp21-14merNA-1
0.1 mMDSSNA-1
Sample conditionsIonic strength: 0 M / Label: p21-14mer / pH: 5.4 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz / Details: Cryoprobe

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNMRCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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