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- PDB-6qh1: The structure of Schizosaccharomyces pombe PCNA in complex with a... -

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Basic information

Entry
Database: PDB / ID: 6qh1
TitleThe structure of Schizosaccharomyces pombe PCNA in complex with an Spd1 derived peptide
Components
  • Proliferating cell nuclear antigen
  • S-phase delaying protein 1
KeywordsDNA BINDING PROTEIN / DNA repair / DNA replication / cell cycle regulation / PCNA-Spd1 complex
Function / homology
Function and homology information


dCDP biosynthetic process / mitotic DNA replication leading strand elongation / ribonucleoside-diphosphate reductase inhibitor activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching / Removal of the Flap Intermediate / Processive synthesis on the lagging strand / SUMOylation of DNA replication proteins / mitotic DNA replication lagging strand elongation / PCNA-Dependent Long Patch Base Excision Repair ...dCDP biosynthetic process / mitotic DNA replication leading strand elongation / ribonucleoside-diphosphate reductase inhibitor activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching / Removal of the Flap Intermediate / Processive synthesis on the lagging strand / SUMOylation of DNA replication proteins / mitotic DNA replication lagging strand elongation / PCNA-Dependent Long Patch Base Excision Repair / Translesion synthesis by REV1 / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / : / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / : / positive regulation of DNA-directed DNA polymerase activity / PCNA complex / DNA damage tolerance / UV-damage excision repair / error-free translesion synthesis / DNA strand elongation involved in DNA replication / DNA repair-dependent chromatin remodeling / DNA polymerase processivity factor activity / leading strand elongation / nuclear replication fork / error-prone translesion synthesis / mismatch repair / translesion synthesis / protein-membrane adaptor activity / positive regulation of DNA replication / positive regulation of DNA repair / intracellular protein localization / site of double-strand break / cell division / chromatin / protein-containing complex binding / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribonucleotide reductase inhibitor / Ribonucleotide reductase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 ...Ribonucleotide reductase inhibitor / Ribonucleotide reductase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / S-phase delaying protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKragelund, B.B. / Nielsen, O. / Olsen, J.G. / Kassem, N. / Prestel, A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4481-00344 Denmark
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs.
Authors: Olsen, J.G. / Prestel, A. / Kassem, N. / Broendum, S.S. / Shamim, H.M. / Simonsen, S. / Grysbaek, M. / Mortensen, J. / Rytkjaer, L.L. / Haxholm, G.W. / Marabini, R. / Holmberg, C. / Carr, A. ...Authors: Olsen, J.G. / Prestel, A. / Kassem, N. / Broendum, S.S. / Shamim, H.M. / Simonsen, S. / Grysbaek, M. / Mortensen, J. / Rytkjaer, L.L. / Haxholm, G.W. / Marabini, R. / Holmberg, C. / Carr, A.M. / Crehuet, R. / Nielsen, O. / Kragelund, B.B.
History
DepositionJan 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
D: S-phase delaying protein 1


Theoretical massNumber of molelcules
Total (without water)88,0414
Polymers88,0414
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-21 kcal/mol
Surface area34310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.860, 71.650, 84.020
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA1 - 2531 - 253
21METMETBB1 - 2531 - 253
12LEULEUAA2 - 2532 - 253
22LEULEUCC2 - 2532 - 253
13LEULEUBB2 - 2532 - 253
23LEULEUCC2 - 2532 - 253

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28996.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: pcn1, pcn, SPBC16D10.09 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03392
#2: Protein/peptide S-phase delaying protein 1 / Protein p14


Mass: 1050.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10585
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM TRIS-HCl pH 7.5, 18% (w/v) PEG4000 and 6% (v/v) glycerol, in the presence of 1.9 mM Spd1(27-46). [PCNA]=0.17 mM (5 mg/mL)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.9→75.7 Å / Num. obs: 19183 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.991 / Net I/σ(I): 6.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.096 / Rpim(I) all: 0.552 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGW

3wgw


Resolution: 2.9→75.68 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.911 / SU B: 27.551 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 980 5.1 %RANDOM
Rwork0.23415 ---
obs0.2356 18195 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å21.32 Å2
2--0.23 Å20 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.9→75.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5797 0 0 0 5797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195861
X-RAY DIFFRACTIONr_bond_other_d0.0090.025721
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.9847917
X-RAY DIFFRACTIONr_angle_other_deg1.878313185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.90825.504258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.653151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7361530
X-RAY DIFFRACTIONr_chiral_restr0.1010.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026533
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021217
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_it5.2497.7062974
X-RAY DIFFRACTIONr_mcbond_other5.2447.7052973
X-RAY DIFFRACTIONr_mcangle_it8.53511.5573700
X-RAY DIFFRACTIONr_mcangle_other8.53511.5583701
X-RAY DIFFRACTIONr_scbond_it6.8968.6682887
X-RAY DIFFRACTIONr_scbond_other6.8958.6692888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.38812.6424218
X-RAY DIFFRACTIONr_long_range_B_refined16.99873.32522644
X-RAY DIFFRACTIONr_long_range_B_other16.99873.32522644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A273680.14
12B273680.14
21A264200.15
22C264200.15
31B269280.15
32C269280.15
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 68 -
Rwork0.395 1326 -
obs--99.08 %

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