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- PDB-8f5q: Crystal structure of human PCNA in complex with the PIP box of FBH1 -

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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


negative regulation of chromatin binding / 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 / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity ...negative regulation of chromatin binding / 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 / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / DNA translocase activity / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / DNA 3'-5' helicase / DNA catabolic process / replisome / SCF ubiquitin ligase complex / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / 3'-5' DNA helicase activity / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / negative regulation of double-strand break repair via homologous recombination / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / DNA helicase activity / epithelial cell differentiation / positive regulation of DNA repair / isomerase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / single-stranded DNA binding / double-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / nuclear body / protein ubiquitination / positive regulation of protein phosphorylation / DNA repair / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / 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 / AAA domain / DNA helicase, UvrD/REP type / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / AAA domain / DNA helicase, UvrD/REP type / F-box domain profile. / F-box-like domain superfamily / F-box-like / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.43 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

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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

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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

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