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- PDB-8q7i: PCNA from Chaetomium thermophilum in complex with Fen1 peptide -

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Basic information

Entry
Database: PDB / ID: 8q7i
TitlePCNA from Chaetomium thermophilum in complex with Fen1 peptide
Components
  • Flap endonuclease 1
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / DNA clamp / DNA replication / homotrimer
Function / homology
Function and homology information


5'-flap endonuclease activity / PCNA complex / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / translesion synthesis / mismatch repair / base-excision repair ...5'-flap endonuclease activity / PCNA complex / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / translesion synthesis / mismatch repair / base-excision repair / Hydrolases; Acting on ester bonds / nucleolus / magnesium ion binding / mitochondrion / DNA binding / nucleoplasm
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Proliferating cell nuclear antigen signature 2. / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 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 / PIN-like domain superfamily / :
Similarity search - Domain/homology
Flap endonuclease 1 / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAlphey, M.S. / Wolford, C.B. / MacNeill, S.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Carnegie Trust for the Universities of Scotland70668 United Kingdom
CitationJournal: Front Mol Biosci / Year: 2023
Title: Canonical binding of Chaetomium thermophilum DNA polymerase delta / zeta subunit PolD3 and flap endonuclease Fen1 to PCNA.
Authors: Alphey, M.S. / Wolford, C.B. / MacNeill, S.A.
History
DepositionAug 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
P: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5234
Polymers30,4772
Non-polymers462
Water5,044280
1
A: Proliferating cell nuclear antigen
P: Flap endonuclease 1
hetero molecules

A: Proliferating cell nuclear antigen
P: Flap endonuclease 1
hetero molecules

A: Proliferating cell nuclear antigen
P: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,56812
Polymers91,4306
Non-polymers1386
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area10020 Å2
ΔGint-90 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.354, 87.354, 214.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28813.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Some residues truncated or omitted from model due to flexibility
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / Gene: CTHT_0061010 / Plasmid: pEHISTEV-CtPCNA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 (pLysS) / References: UniProt: G0SF70
#2: Protein/peptide Flap endonuclease 1 / FEN-1 / Flap structure-specific endonuclease 1


Mass: 1662.928 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Some residues truncated or omitted from model due to flexibility
Source: (synth.) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S2B5, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50mM Tris-HCl pH8.0, 150mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 20, 2023 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→21.86 Å / Num. obs: 23349 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 0.98 / Net I/σ(I): 23.8 / Num. measured all: 247082
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.7 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.182 / Num. measured all: 13994 / Num. unique obs: 1631 / CC1/2: 0.988 / Rpim(I) all: 0.065 / Rrim(I) all: 0.193 / Χ2: 1 / Net I/σ(I) obs: 11.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→21.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.861 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20376 1277 5.5 %RANDOM
Rwork0.17094 ---
obs0.17275 22067 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å2-0 Å2
2--0.26 Å20 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.95→21.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 2 280 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162024
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.6332868
X-RAY DIFFRACTIONr_angle_other_deg0.3791.5644677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.34959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09610380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2281.5251086
X-RAY DIFFRACTIONr_mcbond_other1.2281.5251086
X-RAY DIFFRACTIONr_mcangle_it2.0472.7231357
X-RAY DIFFRACTIONr_mcangle_other2.0472.7261358
X-RAY DIFFRACTIONr_scbond_it1.8671.7631025
X-RAY DIFFRACTIONr_scbond_other1.8661.7651026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.023.1441506
X-RAY DIFFRACTIONr_long_range_B_refined4.87416.292322
X-RAY DIFFRACTIONr_long_range_B_other4.53215.12232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 96 -
Rwork0.166 1590 -
obs--99.65 %

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