[English] 日本語
Yorodumi
- PDB-8f5q: Crystal structure of human PCNA in complex with the PIP box of FBH1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f5q
TitleCrystal structure of human PCNA in complex with the PIP box of FBH1
Components
  • F-box DNA helicase 1
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / Complex
Function / homology
Function and homology information


response to intra-S DNA damage checkpoint signaling / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / DNA translocase activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching ...response to intra-S DNA damage checkpoint signaling / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / DNA translocase activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Processive synthesis on the lagging strand / Telomere C-strand (Lagging Strand) Synthesis / PCNA complex / Removal of the Flap Intermediate / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / DNA catabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Processive synthesis on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / SCF ubiquitin ligase complex / DNA 3'-5' helicase / response to dexamethasone / 3'-5' DNA helicase activity / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / isomerase activity / negative regulation of double-strand break repair via homologous recombination / translesion synthesis / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / DNA helicase activity / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / positive regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / nuclear estrogen receptor binding / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / positive regulation of protein phosphorylation / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / double-stranded DNA binding / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / nuclear body / DNA repair / DNA damage response / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / Proliferating cell nuclear antigen signature 2. ...UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box 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 / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proliferating cell nuclear antigen / F-box DNA helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, J. / Chaves-Arquero, B. / Wei, P. / Tencer, H. / Zhang, G. / Blanco, F. / Kutateladze, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: Molecular insight into the PCNA-binding mode of FBH1.
Authors: Liu, J. / Chaves-Arquero, B. / Wei, P. / Tencer, A.H. / Ruiz-Albor, A. / Zhang, G. / Blanco, F.J. / Kutateladze, T.G.
History
DepositionNov 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: F-box DNA helicase 1
C: Proliferating cell nuclear antigen
D: F-box DNA helicase 1
E: Proliferating cell nuclear antigen
F: F-box DNA helicase 1


Theoretical massNumber of molelcules
Total (without water)89,3376
Polymers89,3376
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.950, 82.210, 118.558
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Proliferating cell nuclear antigen / PCNA / Cyclin


Mass: 28651.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Protein/peptide F-box DNA helicase 1 / hFBH1 / F-box only protein 18


Mass: 1127.292 Da / Num. of mol.: 3 / Fragment: PIP box (UNP residues 56-64) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NFZ0, DNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride, 30% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.28 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.9→41.79 Å / Num. obs: 62010 / % possible obs: 98.28 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.04254 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 11431 / CC1/2: 0.567

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5IY4

5iy4


Resolution: 1.9→41.79 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1997 3.28 %
Rwork0.2241 --
obs0.2254 60944 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 0 0 253 6012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135860
X-RAY DIFFRACTIONf_angle_d2.267903
X-RAY DIFFRACTIONf_dihedral_angle_d14.952787
X-RAY DIFFRACTIONf_chiral_restr0.075935
X-RAY DIFFRACTIONf_plane_restr0.0111002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.36911440.35634144X-RAY DIFFRACTION98
1.95-20.34091390.31454205X-RAY DIFFRACTION98
2-2.060.31721550.29144171X-RAY DIFFRACTION98
2.06-2.130.34571400.2814147X-RAY DIFFRACTION98
2.13-2.20.26441410.2474238X-RAY DIFFRACTION99
2.2-2.290.29781330.26394207X-RAY DIFFRACTION98
2.29-2.390.34381250.24334232X-RAY DIFFRACTION99
2.39-2.520.251500.23844227X-RAY DIFFRACTION99
2.52-2.680.25841380.22134230X-RAY DIFFRACTION99
2.68-2.880.26611470.22824256X-RAY DIFFRACTION99
2.88-3.170.26851510.21924253X-RAY DIFFRACTION99
3.17-3.630.27231410.20014266X-RAY DIFFRACTION99
3.63-4.580.23621580.17724279X-RAY DIFFRACTION99
4.58-41.790.22061350.20924092X-RAY DIFFRACTION93

+
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://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