[English] 日本語
Yorodumi
- PDB-8thw: Cac1 PIP motif bound to PCNA -

+
Open data


ID or keywords:

Loading...

-
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 POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / PCNA complex / 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 / DNA polymerase processivity factor activity / leading strand elongation / Dual incision in TC-NER / chromosome, centromeric region / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more