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- PDB-5iy4: Crystal structure of human PCNA in complex with the PIP box of DVC1 -

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Basic information

Entry
Database: PDB / ID: 5iy4
TitleCrystal structure of human PCNA in complex with the PIP box of DVC1
Components
  • DVC1 PIP box
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / PCNA / PIP box / DVC1
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 / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / MutLalpha complex binding / Polymerase switching / 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 / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / MutLalpha complex binding / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / 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 / protein-DNA covalent cross-linking repair / Removal of the Flap Intermediate from the C-strand / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / replisome / K63-linked polyubiquitin modification-dependent protein binding / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / response to dexamethasone / leading strand elongation / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / protein autoprocessing / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / polyubiquitin modification-dependent protein binding / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / response to UV / epithelial cell differentiation / positive regulation of DNA repair / 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 / ubiquitin binding / positive regulation of protein ubiquitination / 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 / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / metalloendopeptidase activity / 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 / nuclear speck / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
SprT-like / SprT-like domain-containing protein Spartan / SprT-like family / SprT homologues. / Rad18-like CCHC zinc finger / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...SprT-like / SprT-like domain-containing protein Spartan / SprT-like family / SprT homologues. / Rad18-like CCHC zinc finger / 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 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / : / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / DNA-dependent metalloprotease SPRTN
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.945 Å
AuthorsJiang, T. / Xu, M. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Strategic Priority Research ProgramXDB08010301 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of human PCNA in complex with the PIP box of DVC1
Authors: Wang, Y. / Xu, M. / Jiang, T.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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: DVC1 PIP box
C: Proliferating cell nuclear antigen
D: DVC1 PIP box
E: Proliferating cell nuclear antigen
F: DVC1 PIP box


Theoretical massNumber of molelcules
Total (without water)95,5686
Polymers95,5686
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-43 kcal/mol
Surface area34960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.647, 71.647, 322.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 30005.037 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 DVC1 PIP box


Mass: 1850.986 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9H040*PLUS

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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: 1.97 Å3/Da / Density % sol: 43.14 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.1 M Sodium citrate tribasic dehydrates (pH 5.0), 30% v/v Jeffamine ED-2001 (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.945→48.33 Å / Num. obs: 18902 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.34
Reflection shellResolution: 2.95→3 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.77 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U7B

1u7b


Resolution: 2.945→48.329 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.62
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2703 919 5.16 %
Rwork0.2071 --
obs0.2103 17810 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.945→48.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6099 0 0 0 6099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136185
X-RAY DIFFRACTIONf_angle_d1.4638350
X-RAY DIFFRACTIONf_dihedral_angle_d15.0142301
X-RAY DIFFRACTIONf_chiral_restr0.06984
X-RAY DIFFRACTIONf_plane_restr0.0071069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9454-3.10070.3111090.23051762X-RAY DIFFRACTION71
3.1007-3.29490.31111240.24462302X-RAY DIFFRACTION93
3.2949-3.54920.29051520.22222455X-RAY DIFFRACTION99
3.5492-3.90630.28191370.21462498X-RAY DIFFRACTION100
3.9063-4.47120.24791260.2032551X-RAY DIFFRACTION100
4.4712-5.63180.23691420.18062566X-RAY DIFFRACTION100
5.6318-48.33530.2731290.20292757X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.2113 Å / Origin y: -38.456 Å / Origin z: -38.7756 Å
111213212223313233
T0.2134 Å20.1281 Å2-0.0108 Å2-0.1672 Å2-0.031 Å2--0.3144 Å2
L1.1258 °20.5756 °20.2398 °2-1.0254 °20.0802 °2--2.1801 °2
S0.0473 Å °0.1067 Å °0.0395 Å °0.0565 Å °-0.0274 Å °0.0172 Å °-0.0206 Å °0.254 Å °-0.0221 Å °
Refinement TLS groupSelection details: all

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