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- PDB-2zvm: Crystal structure of PCNA in complex with DNA polymerase iota fragment -

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Basic information

Entry
Database: PDB / ID: 2zvm
TitleCrystal structure of PCNA in complex with DNA polymerase iota fragment
Components
  • DNA polymerase iota
  • Proliferating cell nuclear antigen
KeywordsTRANSFERASE / DNA replication / PCNA / clamp / translesion synthesis / TLS / DNA polymerase / complex / PIP-box / DNA polymerase iota
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 / Processive synthesis on the lagging strand ...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 / Processive synthesis on the lagging strand / Telomere C-strand (Lagging Strand) Synthesis / PCNA complex / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Processive synthesis on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / positive regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / nuclear estrogen receptor binding / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHishiki, A. / Hashimoto, H. / Hanafusa, T. / Kamei, K. / Ohashi, E. / Shimizu, T. / Ohmori, H. / Sato, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Basis for Novel Interactions between Human Translesion Synthesis Polymerases and Proliferating Cell Nuclear Antigen
Authors: Hishiki, A. / Hashimoto, H. / Hanafusa, T. / Kamei, K. / Ohashi, E. / Shimizu, T. / Ohmori, H. / Sato, M.
History
DepositionNov 11, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 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
U: DNA polymerase iota
B: Proliferating cell nuclear antigen
V: DNA polymerase iota
C: Proliferating cell nuclear antigen
W: DNA polymerase iota


Theoretical massNumber of molelcules
Total (without water)94,0286
Polymers94,0286
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-44.3 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.620, 68.820, 90.180
Angle α, β, γ (deg.)90.00, 95.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28795.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12004
#2: Protein/peptide DNA polymerase iota


Mass: 2546.958 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemically synthesized peptide / References: DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: hanging drop vapor diffusion / pH: 6.4
Details: pH6.4, HANGING DROP VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2007 / Details: Rhodium coated silicon single crystal mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 44815 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4440 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYM

1vym


Resolution: 2.3→19.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.736 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2249 5 %RANDOM
Rwork0.19335 ---
obs0.19627 42715 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20.43 Å2
2--0.4 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 0 225 6210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225948
X-RAY DIFFRACTIONr_bond_other_d00.023961
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9868027
X-RAY DIFFRACTIONr_angle_other_deg4.4239729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.16725.265226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8531522
X-RAY DIFFRACTIONr_chiral_restr0.1050.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026526
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021093
X-RAY DIFFRACTIONr_nbd_refined0.2110.21050
X-RAY DIFFRACTIONr_nbd_other0.2410.23711
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22728
X-RAY DIFFRACTIONr_nbtor_other0.1180.23101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3850.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5331.54907
X-RAY DIFFRACTIONr_mcbond_other0.0271.51565
X-RAY DIFFRACTIONr_mcangle_it1.7826151
X-RAY DIFFRACTIONr_scbond_it2.84132410
X-RAY DIFFRACTIONr_scangle_it4.2414.51876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 143 -
Rwork0.225 2700 -
obs--100 %
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)
11.7060.2747-0.18030.43470.28431.01030.0133-0.07570.1231-0.0079-0.02170.088-0.17050.03450.0084-0.0962-0.03190.0776-0.042-0.0326-0.018524.79915.9743.885
217.4356-12.3148-6.816813.079110.2039.2921-0.338-1.15850.32780.86560.4714-0.24470.42110.8108-0.13340.0035-0.05720.07310.2116-0.0166-0.033634.42216.20662.417
31.1325-0.3301-1.11420.86340.86771.9414-0.06120.0679-0.0196-0.12530.03810.0065-0.0464-0.07860.0232-0.1232-0.06790.0655-0.0003-0.06630.003810.268-14.1415.305
418.86456.35443.01199.3994-0.46118.5497-0.46310.1496-0.9224-0.23270.27-0.16161.0366-0.28670.1931-0.103-0.09710.11520.0355-0.0361-0.0038-1.153-25.93926.82
51.44010.81420.01181.35260.66180.9559-0.038-0.0442-0.1366-0.0635-0.0079-0.06730.00170.09690.046-0.1386-0.04420.07080.0190.0235-0.053552.473-2.47215.532
618.6812.99024.01959.03764.91824.330.03980.2651-0.31360.681-0.1068-0.20540.74530.96690.06690.03780.15190.08980.01290.0529-0.003462.297-19.27414.14
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION2U420 - 432
3X-RAY DIFFRACTION3B1 - 255
4X-RAY DIFFRACTION4V420 - 429
5X-RAY DIFFRACTION5C1 - 256
6X-RAY DIFFRACTION6W421 - 429

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