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- PDB-8thw: Cac1 PIP motif bound to PCNA -

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Basic information

Entry
Database: PDB / ID: 8thw
TitleCac1 PIP motif bound to PCNA
ComponentsProliferating cell nuclear antigen,Chromatin assembly factor 1 subunit p90
KeywordsPROTEIN BINDING / Sliding clamp / histone chaperone / replication-coupled nucleosome assembly / chromatin assembly / gene silencing / protein complex / PIP
Function / homology
Function and homology information


CAF-1 complex / 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 / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats ...CAF-1 complex / 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 / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / PCNA complex / Translesion Synthesis by POLH / DNA replication-dependent chromatin assembly / establishment of mitotic sister chromatid cohesion / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / leading strand elongation / DNA polymerase processivity factor activity / chromosome, centromeric region / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / nucleotide-excision repair / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / DNA replication / chromosome, telomeric region / DNA repair / chromatin / DNA binding / identical protein binding / nucleus
Similarity search - Function
: / Chromatin assembly factor 1 subunit Cac1, C-terminal domain / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / 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 ...: / Chromatin assembly factor 1 subunit Cac1, C-terminal domain / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / 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 / :
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Chromatin assembly factor 1 subunit p90
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVeltri, E. / Hoitsma, N.M. / Dieckman, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2047553 United States
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Basis for the Interaction Between Yeast Chromatin Assembly Factor 1 and Proliferating Cell Nuclear Antigen.
Authors: Orndorff, K.S. / Veltri, E.J. / Hoitsma, N.M. / Williams, I.L. / Hall, I. / Jaworski, G.E. / Majeres, G.E. / Kallepalli, S. / Vito, A.F. / Struble, L.R. / Borgstahl, G.E.O. / Dieckman, L.M.
History
DepositionJul 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen,Chromatin assembly factor 1 subunit p90
B: Proliferating cell nuclear antigen,Chromatin assembly factor 1 subunit p90
C: Proliferating cell nuclear antigen,Chromatin assembly factor 1 subunit p90


Theoretical massNumber of molelcules
Total (without water)97,1673
Polymers97,1673
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-8 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.615, 87.360, 76.511
Angle α, β, γ (deg.)90.000, 108.330, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Proliferating cell nuclear antigen,Chromatin assembly factor 1 subunit p90 / PCNA / CAF-1 90 kDa subunit / RAP1 localization factor 2


Mass: 32388.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR088C, YBR0811, RLF2, CAC1, YPR018W, YP9531.12
Production host: Escherichia coli (E. coli) / References: UniProt: P15873, UniProt: Q12495

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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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M magnesium acetate tetrahydrate (Mg Ac4H) and 11% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 35223 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 40.21 Å2 / Rrim(I) all: 0.063 / Net I/σ(I): 17.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2 % / Num. unique obs: 1437 / CC1/2: 0.634 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V7K

5v7k


Resolution: 2.6→24.89 Å / SU ML: 0.3569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2674 2862 8.13 %
Rwork0.2162 32355 -
obs0.2204 35217 61.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.91 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 0 0 6315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00866408
X-RAY DIFFRACTIONf_angle_d1.35528625
X-RAY DIFFRACTIONf_chiral_restr0.08121011
X-RAY DIFFRACTIONf_plane_restr0.00891101
X-RAY DIFFRACTIONf_dihedral_angle_d17.16782418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.5104280.3484318X-RAY DIFFRACTION11.71
2.64-2.690.3285410.3049454X-RAY DIFFRACTION17.52
2.69-2.740.3599620.3359698X-RAY DIFFRACTION26.21
2.74-2.80.3855690.3573764X-RAY DIFFRACTION29.4
2.8-2.860.3668780.3328880X-RAY DIFFRACTION33.23
2.86-2.920.3497890.3169997X-RAY DIFFRACTION37.46
2.92-30.3629990.33731089X-RAY DIFFRACTION41.67
3-3.080.37091120.31481217X-RAY DIFFRACTION46.76
3.08-3.170.37371190.32221368X-RAY DIFFRACTION51.99
3.17-3.270.35641430.29191519X-RAY DIFFRACTION57.53
3.27-3.390.28691460.25811673X-RAY DIFFRACTION63.38
3.39-3.520.32471550.24591811X-RAY DIFFRACTION67.82
3.52-3.680.30021720.23382035X-RAY DIFFRACTION76.82
3.68-3.880.30741870.21962203X-RAY DIFFRACTION83.16
3.88-4.120.28562070.20442344X-RAY DIFFRACTION89.16
4.12-4.430.24952280.18152514X-RAY DIFFRACTION95.18
4.43-4.880.21552330.15342623X-RAY DIFFRACTION99.24
4.88-5.580.23552280.18172611X-RAY DIFFRACTION99.34
5.58-70.23912350.21852634X-RAY DIFFRACTION99.62
7-24.890.1822310.1772603X-RAY DIFFRACTION98.44

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