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- PDB-5zut: Crystal Structure of Yeast PCNA in Complex with N24 Peptide -

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Basic information

Entry
Database: PDB / ID: 5zut
TitleCrystal Structure of Yeast PCNA in Complex with N24 Peptide
Components
  • N24
  • Proliferating cell nuclear antigen
KeywordsCELL CYCLE / Yeast PCNA / PI3K / N24 Peptide / Proliferation
Function / homology
Function and homology information


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 / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH ...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 / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / 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 / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / 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 / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / 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 / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Phosphatidylinositol 3-kinase regulatory subunit gamma
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsCheng, X.Y. / Kuang, X.L. / Zhou, Y. / Xia, X.M. / SU, Z.D.
CitationJournal: To Be Published
Title: Crystal Structure of Yeast PCNA in Complex with N24 Peptide
Authors: Cheng, X.Y. / Kuang, X.L. / Zhou, Y. / Xia, X.M. / SU, Z.D.
History
DepositionMay 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 5, 2024Group: Data collection / Category: refln

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
E: N24


Theoretical massNumber of molelcules
Total (without water)34,7812
Polymers34,7812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-12 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.350, 84.030, 58.150
Angle α, β, γ (deg.)90.000, 93.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 32572.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: POL30, YBR088C, YBR0811 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P15873
#2: Protein/peptide N24 / Phosphatidylinositol 3-kinase regulatory subunit gamma


Mass: 2208.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R3 / Production host: unidentified (others) / References: UniProt: Q5T4P3

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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: 2.82 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: n-Octyl-b-D-glu, NaCi pH 5.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→58.03 Å / Num. obs: 9212 / % possible obs: 98.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.133 / Scaling rejects: 73
Reflection scaleGroup code: 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.83-2.97.20.512199.4
12.63-58.036.40.109198.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data collection
PDB_EXTRACT5.8.0222data extraction
XDSdata reduction
Aimless3.24data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B8I, 5DA7

6b8i
PDB Unreleased entry

5da7


Resolution: 2.82→58.03 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.157 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3966 527 5.7 %RANDOM
Rwork0.326 ---
obs0.3301 8684 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120 Å2 / Biso mean: 99.825 Å2 / Biso min: 50.63 Å2
Baniso -1Baniso -2Baniso -3
1-67.58 Å20 Å2114.5 Å2
2---81.24 Å2-0 Å2
3---13.66 Å2
Refinement stepCycle: final / Resolution: 2.82→58.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 0 2155
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0142189
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172059
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.6422953
X-RAY DIFFRACTIONr_angle_other_deg1.3921.6394826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8375271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03324.423104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11815414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.145158
X-RAY DIFFRACTIONr_chiral_restr0.0430.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022397
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02387
X-RAY DIFFRACTIONr_mcbond_it3.49310.1511090
X-RAY DIFFRACTIONr_mcbond_other3.4910.151089
X-RAY DIFFRACTIONr_mcangle_it5.73415.2131359
LS refinement shellResolution: 2.824→2.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.812 23 -
Rwork0.712 672 -
all-695 -
obs--98.44 %

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