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- PDB-1plr: CRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY F... -

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Basic information

Entry
Database: PDB / ID: 1plr
TitleCRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY FACTOR PCNA
ComponentsPROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)
KeywordsDNA-BINDING / NUCLEAR PROTEIN / DNA REPLICATION
Function / homology
Function and homology information


positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 ...positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / DNA damage tolerance / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / Dual incision in TC-NER / translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKrishna, T.S.R. / Kong, X.-P. / Gary, S. / Burgers, P.M. / Kuriyan, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA.
Authors: Krishna, T.S. / Kong, X.P. / Gary, S. / Burgers, P.M. / Kuriyan, J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Proliferating Cell Nuclear Antigen (PCNA) from Saccharomyces Cerevisiae
Authors: Krishna, T.S.R. / Kong, X.-P. / Gary, S. / Burgers, P. / Kuriyan, J.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Sliding Clamps of DNA Polymerases
Authors: Kuriyan, J. / Donnell, M.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: Three-Dimensional Structure of the Beta Subunit of E. Coli DNA Polymerase III Holoenzyme: A Sliding DNA Clamp
Authors: Kong, X.-P. / Onrust, R. / Donnell, M. / Kuriyan, J.
History
DepositionJan 2, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)


Theoretical massNumber of molelcules
Total (without water)28,9441
Polymers28,9441
Non-polymers00
Water18010
1
A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)

A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)

A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)


Theoretical massNumber of molelcules
Total (without water)86,8323
Polymers86,8323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Unit cell
Length a, b, c (Å)121.700, 121.700, 121.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)


Mass: 28944.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P15873
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.19 Å3/Da / Density % sol: 76.3 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown / Details: Krishna, T.S.R., (1994) J.Mol.Biol., 241, 265.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl11
21 mMEDTA11
31 mMDTT11
40.1 M11NaCl
520 mg/mlprotain12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 12273 / % possible obs: 86.3 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / Redundancy: 7.8 % / Num. measured all: 95433 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.05 Å / % possible obs: 80.9 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.218 -
obs0.218 9174
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 10 2040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.04
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

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