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- PDB-1vyj: Structural and biochemical studies of human PCNA complexes provid... -

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Basic information

Entry
Database: PDB / ID: 1vyj
TitleStructural and biochemical studies of human PCNA complexes provide the basis for association with CDK/cyclin and rationale for inhibitor design
Components
  • PROLIFERATING CELL NUCLEAR ANTIGEN
  • SMALL PEPTIDE SAVLQKKITDYFHPKK
KeywordsDNA BINDING PROTEIN / DNA / REPLICATION / PROCESSIVITY / ONCOGENE / DNA-BINDING PROTEIN / DNA REPLICATION / DNA-BINDING SYSTEMIC LUPUS ERYTHEMATOSUS
Function / homology
Function and homology information


positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / positive regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / nuclear estrogen receptor binding / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKontopidis, G. / Wu, S. / Zheleva, D. / Taylor, P. / Mcinnes, C. / Lane, D. / Fischer, P. / Walkinshaw, M.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural and Biochemical Studies of Human Proliferating Cell Nuclear Antigen Complexes Provide a Rationale for Cyclin Association and Inhibitor Design
Authors: Kontopidis, G. / Wu, S. / Zheleva, D. / Taylor, P. / Mcinnes, C. / Lane, D. / Fischer, P. / Walkinshaw, M.D.
History
DepositionApr 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLIFERATING CELL NUCLEAR ANTIGEN
B: SMALL PEPTIDE SAVLQKKITDYFHPKK
C: PROLIFERATING CELL NUCLEAR ANTIGEN
D: SMALL PEPTIDE SAVLQKKITDYFHPKK
E: PROLIFERATING CELL NUCLEAR ANTIGEN
F: SMALL PEPTIDE SAVLQKKITDYFHPKK
G: PROLIFERATING CELL NUCLEAR ANTIGEN
H: SMALL PEPTIDE SAVLQKKITDYFHPKK
I: PROLIFERATING CELL NUCLEAR ANTIGEN
J: SMALL PEPTIDE SAVLQKKITDYFHPKK
K: PROLIFERATING CELL NUCLEAR ANTIGEN
L: SMALL PEPTIDE SAVLQKKITDYFHPKK


Theoretical massNumber of molelcules
Total (without water)184,22412
Polymers184,22412
Non-polymers00
Water5,765320
1
A: PROLIFERATING CELL NUCLEAR ANTIGEN
B: SMALL PEPTIDE SAVLQKKITDYFHPKK
C: PROLIFERATING CELL NUCLEAR ANTIGEN
D: SMALL PEPTIDE SAVLQKKITDYFHPKK
E: PROLIFERATING CELL NUCLEAR ANTIGEN
F: SMALL PEPTIDE SAVLQKKITDYFHPKK


Theoretical massNumber of molelcules
Total (without water)92,1126
Polymers92,1126
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: PROLIFERATING CELL NUCLEAR ANTIGEN
H: SMALL PEPTIDE SAVLQKKITDYFHPKK
I: PROLIFERATING CELL NUCLEAR ANTIGEN
J: SMALL PEPTIDE SAVLQKKITDYFHPKK
K: PROLIFERATING CELL NUCLEAR ANTIGEN
L: SMALL PEPTIDE SAVLQKKITDYFHPKK


Theoretical massNumber of molelcules
Total (without water)92,1126
Polymers92,1126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.101, 119.101, 305.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
PROLIFERATING CELL NUCLEAR ANTIGEN / PCNA / CYCLIN


Mass: 28795.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12004
#2: Protein/peptide
SMALL PEPTIDE SAVLQKKITDYFHPKK


Mass: 1908.266 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN IS AN AUXILIARY PROTEIN OF DNA POLYMERASE DELTA IS INVOLVED IN THE CONTROL OF ...THIS PROTEIN IS AN AUXILIARY PROTEIN OF DNA POLYMERASE DELTA IS INVOLVED IN THE CONTROL OF EUKARYOTIC DNA REPLICATION BY INCREASING THE POLYMERASE'S PROCESSIBILITY DURING ELONGATION OF THE LEADING STRAND.
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 60.7 %
Crystal growpH: 8 / Details: 2.7M AS, HEPES PH8, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8456
DetectorDate: Aug 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8456 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 62908 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1 / % possible all: 98.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXC

1axc


Resolution: 2.8→14 Å / SU B: 13.2 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1917 3.1 %RANDOM
Rwork0.17644 ---
obs0.17897 60068 99.5 %-
Displacement parametersBiso mean: 54.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12712 0 0 320 13032

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