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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 / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / 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 / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Processive synthesis on the C-strand of the telomere / 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 / replisome / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / 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

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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 / 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.

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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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