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- PDB-8p9o: PCNA from Chaetomium thermophilum in complex with PolD3 peptide -

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Basic information

Entry
Database: PDB / ID: 8p9o
TitlePCNA from Chaetomium thermophilum in complex with PolD3 peptide
Components
  • Proliferating cell nuclear antigen
  • Synthetic peptide corresponding to amino acids 437 to 451 of PolD3 from Chaetomium thermophilum
KeywordsREPLICATION / DNA CLAMP / DNA REPLICATION / HOMOTRIMER
Function / homology
Function and homology information


PCNA complex / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA binding
Similarity search - Function
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
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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
DepositionJun 6, 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

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
P: Synthetic peptide corresponding to amino acids 437 to 451 of PolD3 from Chaetomium thermophilum


Theoretical massNumber of molelcules
Total (without water)88,0264
Polymers88,0264
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-27 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.840, 56.391, 62.860
Angle α, β, γ (deg.)90.93, 90.55, 99.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28813.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The first 4 residues remain after affinity tag cleavage. Flexible loops and sidechains have been omitted or truncated.
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 Synthetic peptide corresponding to amino acids 437 to 451 of PolD3 from Chaetomium thermophilum


Mass: 1584.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-terminal residues omitted due to flexibility
Source: (synth.) Thermochaetoides thermophila DSM 1495 (fungus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Phosphate/citrate, pH4.2, 40% v/v PEG300

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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: Feb 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: 2.45→27.57 Å / Num. obs: 25893 / % possible obs: 93.2 % / Redundancy: 2.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.067 / Rrim(I) all: 0.113 / Χ2: 0.61 / Net I/σ(I): 5.7 / Num. measured all: 66712
Reflection shellResolution: 2.45→2.55 Å / % possible obs: 91 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.255 / Num. measured all: 6953 / Num. unique obs: 2840 / CC1/2: 0.881 / Rpim(I) all: 0.197 / Rrim(I) all: 0.324 / Χ2: 0.75 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→27.57 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.529 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 1.157 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24943 1189 4.6 %RANDOM
Rwork0.21283 ---
obs0.2144 24703 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å21.12 Å2-0.18 Å2
2--0.06 Å20.05 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.45→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 0 152 5846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165550
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.6317821
X-RAY DIFFRACTIONr_angle_other_deg0.341.56312777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.67519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.267101007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0460.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
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_it0.8032.0043031
X-RAY DIFFRACTIONr_mcbond_other0.8032.0043031
X-RAY DIFFRACTIONr_mcangle_it1.363.5953770
X-RAY DIFFRACTIONr_mcangle_other1.3613.5963771
X-RAY DIFFRACTIONr_scbond_it0.9322.0992740
X-RAY DIFFRACTIONr_scbond_other0.9312.12741
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5793.8384051
X-RAY DIFFRACTIONr_long_range_B_refined3.00321.565845
X-RAY DIFFRACTIONr_long_range_B_other2.98321.455834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 82 -
Rwork0.279 1762 -
obs--90.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9742-0.1926-0.09270.75420.97533.78460.0310.15080.1374-0.1217-0.02110.024-0.17-0.0057-0.010.02890.00030.01680.01260.00320.0581-23.041411.1208-10.5513
23.3642-0.6996-0.75631.56530.2962.20130.02490.279-0.1543-0.1563-0.07280.03780.1377-0.09170.04790.0312-0.00620.0080.0549-0.04170.0385-11.8241-8.9526-23.6291
38.55660.48650.52085.13572.87746.90740.3534-0.58530.15360.2533-0.3724-0.02060.2839-0.32960.0190.13540.05050.03190.14530.0140.018312.8709-17.8558-10.253
41.16070.38831.02861.09790.44122.7410.1460.1424-0.0772-0.0232-0.0857-0.00910.37750.0624-0.06030.07150.01130.02240.0448-0.03820.094119.4536-15.0557-0.7453
52.6931-2.2930.03783.4312-1.28221.8674-0.07840.0482-0.08330.0358-0.0484-0.03420.05450.04920.12680.057-0.06620.04430.1039-0.0650.058310.58211.044824.4047
62.8810.46671.05821.8145-0.95442.997-0.0533-0.16480.3749-0.0460.02120.0468-0.2105-0.00420.0320.0354-0.02190.0230.0363-0.05270.0862-12.704319.417714.2185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 121
2X-RAY DIFFRACTION2A122 - 255
3X-RAY DIFFRACTION3B1 - 25
4X-RAY DIFFRACTION4B26 - 255
5X-RAY DIFFRACTION5C1 - 122
6X-RAY DIFFRACTION6C123 - 255

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