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- PDB-4ztd: Crystal Structure of Human PCNA in complex with a TRAIP peptide -

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Basic information

Entry
Database: PDB / ID: 4ztd
TitleCrystal Structure of Human PCNA in complex with a TRAIP peptide
Components
  • ALA-GLY-ALA-GLY-ALA
  • ALA-PHE-GLN-ALA-LYS-LEU-ASP-THR-PHE-LEU-TRP-SER
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / TRAIP / complex
Function / homology
Function and homology information


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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis ...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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / negative regulation of interferon-beta production / Processive synthesis on the lagging strand / PCNA complex / protein-DNA covalent cross-linking repair / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / site of DNA damage / SUMOylation of DNA replication proteins / negative regulation of tumor necrosis factor-mediated signaling pathway / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / male germ cell nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / replication fork / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / nuclear body / apoptotic process / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular exosome / nucleoplasm / metal ion binding / identical protein binding / nucleus
Similarity search - Function
: / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Ring finger 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 ...: / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Ring finger 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 / : / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / E3 ubiquitin-protein ligase TRAIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsMontoya, G. / Mortuza, G.B. / Blanco, F.J. / Ibanez de Opakua, A.
Citation
Journal: J.Cell Biol. / Year: 2016
Title: TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress.
Authors: Hoffmann, S. / Smedegaard, S. / Nakamura, K. / Mortuza, G.B. / Raschle, M. / Ibanez de Opakua, A. / Oka, Y. / Feng, Y. / Blanco, F.J. / Mann, M. / Montoya, G. / Groth, A. / Bekker-Jensen, S. / Mailand, N.
#1: Journal: Nat Commun / Year: 2015
Title: Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair.
Authors: De Biasio, A. / de Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. ...Authors: De Biasio, A. / de Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. / Montoya, G. / Blanco, F.J.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: ALA-PHE-GLN-ALA-LYS-LEU-ASP-THR-PHE-LEU-TRP-SER
E: ALA-PHE-GLN-ALA-LYS-LEU-ASP-THR-PHE-LEU-TRP-SER
F: ALA-GLY-ALA-GLY-ALA


Theoretical massNumber of molelcules
Total (without water)86,9156
Polymers86,9156
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-24 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.360, 84.360, 210.862
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 27904.836 Da / Num. of mol.: 3 / Fragment: UNP residues 2-254
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 ALA-PHE-GLN-ALA-LYS-LEU-ASP-THR-PHE-LEU-TRP-SER


Mass: 1427.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BWF2*PLUS
#3: Protein/peptide ALA-GLY-ALA-GLY-ALA


Mass: 345.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 6K in 0.1mM magnesium acetate, MES buffer pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.11
ReflectionResolution: 2.199→42.749 Å / Num. obs: 42654 / % possible obs: 99.17 % / Redundancy: 8 % / Rmerge(I) obs: 0.06399 / Net I/σ(I): 22.17
Reflection shellResolution: 2.199→2.2519 Å / Rmerge(I) obs: 0.7153

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2G

4d2g


Resolution: 2.199→42.749 Å / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 28.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2338 2144 5.03 %
Rwork0.2035 40516 -
obs0.2045 42654 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.61 Å2 / Biso mean: 56.6074 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.199→42.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 0 188 6245
Biso mean---55.74 -
Num. residues----787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056140
X-RAY DIFFRACTIONf_angle_d0.9998295
X-RAY DIFFRACTIONf_chiral_restr0.036977
X-RAY DIFFRACTIONf_plane_restr0.0041064
X-RAY DIFFRACTIONf_dihedral_angle_d16.8682277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2007-2.25190.29871330.26962519265288
2.2519-2.30820.27771410.26772671281294
2.3082-2.37060.27251420.25182709285195
2.3706-2.44030.28081420.24692705284795
2.4403-2.51910.2561430.24782718286195
2.5191-2.60910.24761420.2382719286195
2.6091-2.71350.27821430.23882703284695
2.7135-2.8370.27241420.24582707284995
2.837-2.98650.30151440.22752729287395
2.9865-3.17360.2351420.21672700284295
3.1736-3.41850.25231440.19952723286795
3.4185-3.76240.2091430.18982712285595
3.7624-4.30630.22231430.17342724286795
4.3063-5.42370.19561440.15072731287595
5.4237-42.18770.21861460.2192746289295

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