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- PDB-1u7b: Crystal structure of hPCNA bound to residues 331-350 of the flap ... -

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Basic information

Entry
Database: PDB / ID: 1u7b
TitleCrystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1)
Components
  • Proliferating cell nuclear antigen
  • SRQGSTQGRLDDFFKVTGSL peptide of Flap endonuclease-1
KeywordsREPLICATION / flap endonuclease / sliding clamp / DNA processing / FEN1 / PIP-Box
Function / homology
Function and homology information


positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / nucleic acid metabolic process / double-stranded DNA exodeoxyribonuclease activity / 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 sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / nucleic acid metabolic process / double-stranded DNA exodeoxyribonuclease activity / 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 / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / UV protection / 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 / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / replisome / 5'-3' exonuclease activity / exonuclease activity / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / replication fork processing / response to dexamethasone / leading strand elongation / Early Phase of HIV Life Cycle / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / replication fork / male germ cell nucleus / nuclear estrogen receptor binding / liver regeneration / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / memory / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / double-strand break repair / RNA-DNA hybrid ribonuclease activity / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA replication / damaged DNA binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nuclear body / DNA repair / centrosome / chromatin binding / protein-containing complex binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / enzyme binding / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding
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 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 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 / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBruning, J.B. / Shamoo, Y.
CitationJournal: Structure / Year: 2004
Title: Structural and Thermodynamic Analysis of Human PCNA with Peptides Derived from DNA Polymerase-delta p66 Subunit and Flap Endonuclease-1.
Authors: Bruning, J.B. / Shamoo, Y.
History
DepositionAug 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: SRQGSTQGRLDDFFKVTGSL peptide of Flap endonuclease-1


Theoretical massNumber of molelcules
Total (without water)30,9982
Polymers30,9982
Non-polymers00
Water2,414134
1
A: Proliferating cell nuclear antigen
B: SRQGSTQGRLDDFFKVTGSL peptide of Flap endonuclease-1

A: Proliferating cell nuclear antigen
B: SRQGSTQGRLDDFFKVTGSL peptide of Flap endonuclease-1

A: Proliferating cell nuclear antigen
B: SRQGSTQGRLDDFFKVTGSL peptide of Flap endonuclease-1


Theoretical massNumber of molelcules
Total (without water)92,9946
Polymers92,9946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_535-y,x-y-2,z1
crystal symmetry operation3_755-x+y+2,-x,z1
Unit cell
Length a, b, c (Å)81.498, 81.498, 67.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 28795.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pET28a-hPCNA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P12004
#2: Protein/peptide SRQGSTQGRLDDFFKVTGSL peptide of Flap endonuclease-1


Mass: 2202.406 Da / Num. of mol.: 1 / Fragment: PIP-box region of FEN-1 (residues 331-350) / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN Homo sapiens (Human)
References: UniProt: P39748
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.09 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 29, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. all: 20438 / Num. obs: 20438 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.27 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 43.5
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 6.42 / Num. unique all: 266 / Rsym value: 0.0642 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1AXC.pdb without chains B,D,F

1axc


Resolution: 1.88→9.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 865515.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 817 4.8 %RANDOM
Rwork0.217 ---
obs0.217 17160 83 %-
all-17160 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.5198 Å2 / ksol: 0.521453 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.63 Å2-1.37 Å20 Å2
2---5.63 Å20 Å2
3---11.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-10 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.88→9.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 0 134 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.273
X-RAY DIFFRACTIONc_mcangle_it4.314
X-RAY DIFFRACTIONc_scbond_it7.136
X-RAY DIFFRACTIONc_scangle_it9.387.5
LS refinement shellResolution: 1.88→1.92 Å / Rfactor Rfree error: 0.076 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.373 24 6.2 %
Rwork0.307 360 -
obs-266 18 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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