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- PDB-2zvl: Crystal structure of PCNA in complex with DNA polymerase kappa fr... -

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Basic information

Entry
Database: PDB / ID: 2zvl
TitleCrystal structure of PCNA in complex with DNA polymerase kappa fragment
Components
  • DNA polymerase kappaPOLK
  • Proliferating cell nuclear antigen
KeywordsTRANSFERASE / DNA replication / PCNA / clamp / translesion synthesis / TLS / DNA polymerase / TLS polymerase / complex / PIP-box / DNA polymerase kappa
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 / MutLalpha complex binding / nuclear lamina / 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 / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / Translesion synthesis by REV1 / Translesion synthesis by POLK / 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 / replication fork / positive regulation of DNA replication / 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 / 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 / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / 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: 2.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 kappa
B: Proliferating cell nuclear antigen
V: DNA polymerase kappa
C: Proliferating cell nuclear antigen
W: DNA polymerase kappa
D: Proliferating cell nuclear antigen
X: DNA polymerase kappa
E: Proliferating cell nuclear antigen
Y: DNA polymerase kappa
F: Proliferating cell nuclear antigen
Z: DNA polymerase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,73922
Polymers182,96312
Non-polymers77710
Water2,162120
1
A: Proliferating cell nuclear antigen
U: DNA polymerase kappa
B: Proliferating cell nuclear antigen
V: DNA polymerase kappa
C: Proliferating cell nuclear antigen
W: DNA polymerase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,87011
Polymers91,4816
Non-polymers3885
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-158.7 kcal/mol
Surface area38000 Å2
2
D: Proliferating cell nuclear antigen
X: DNA polymerase kappa
E: Proliferating cell nuclear antigen
Y: DNA polymerase kappa
F: Proliferating cell nuclear antigen
Z: DNA polymerase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,87011
Polymers91,4816
Non-polymers3885
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-159.9 kcal/mol
Surface area37190 Å2
Unit cell
Length a, b, c (Å)74.769, 74.707, 109.049
Angle α, β, γ (deg.)87.25, 77.46, 80.26
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28795.752 Da / Num. of mol.: 6
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 kappa / POLK


Mass: 1698.014 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: chemically synthesized peptide / References: DNA-directed DNA polymerase
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: hanging drop vapor diffusion / pH: 5.2
Details: pH5.2, HANGING DROP VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU MSC JUPITER 210 / Detector: CCD / Date: Oct 3, 2006 / Details: mirrors
RadiationMonochromator: Si double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 71006 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 4.1 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYM

1vym


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.09 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28943 3575 5 %RANDOM
Rwork0.22542 ---
obs0.22865 67254 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: 37.715 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.1 Å20.45 Å2
2---0.12 Å20.19 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11928 0 26 120 12074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211699
X-RAY DIFFRACTIONr_bond_other_d00.0210838
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.98115821
X-RAY DIFFRACTIONr_angle_other_deg1.235325137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.951522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48825.175429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.307152022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5371538
X-RAY DIFFRACTIONr_chiral_restr0.1010.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212886
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022170
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_it1.3171.57628
X-RAY DIFFRACTIONr_mcbond_other0.3491.53137
X-RAY DIFFRACTIONr_mcangle_it2.305212209
X-RAY DIFFRACTIONr_scbond_it3.48434071
X-RAY DIFFRACTIONr_scangle_it5.4024.53612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 207 -
Rwork0.265 4332 -
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)
11.38010.894-0.33731.4399-0.25070.7516-0.15660.1293-0.033-0.1770.10260.00290.05040.00040.0540.0809-0.00370.10520.01680.0220.1926-12.513-1.635-44.312
20.89090.22770.42441.54190.65651.2780.0526-0.0139-0.03470.0319-0.03120.01310.0048-0.0277-0.02150.05020.02890.0980.02010.06410.2144-40.912.643-14.493
31.4458-0.3553-0.59930.760.46851.04210.034-0.13090.05180.01850.0105-0.0463-0.02340.0969-0.04450.03520.0130.07920.02770.04140.1957-3.7934.418-21.728
41.62030.7181-0.23591.0971-0.38420.60530.0912-0.1125-0.03250.0903-0.1179-0.0454-0.01960.02790.02670.05510.00740.0830.02150.03910.163434.516-25.09743.984
51.51430.01830.72470.72030.28931.4682-0.01820.08740.04560.02510.0206-0.0108-0.0050.0586-0.00250.05470.02580.10920.01850.05610.22825.1545.08613.806
60.639-0.40090.26111.5082-0.57730.93070.01120.037-0.0468-0.06310.05170.0560.0619-0.0322-0.06290.04890.00350.09260.00860.01630.2178-2.521-27.85321.198
77.32171.59060.19810.34570.04350.007-1.23292.5336-0.0838-0.33690.8873-0.0151-0.02940.06990.34550.5338-0.55110.12940.8816-0.02420.0826-9.1260.406-62.63
82.66492.29-0.29472.2065-1.39946.742-0.1006-0.0011-0.0866-0.10910.0280.01390.04240.07940.07250.01820.00170.01180.02530.06360.2552-57.9913.782-21.664
98.08771.0672.74835.31731.02314.67880.0606-0.23410.37130.1693-0.00040.0556-0.3841-0.4262-0.06010.07160.04870.08360.04510.03830.2312-8.50652.349-24.026
104.16461.20926.31336.47264.028310.3579-0.07510.12030.00811.16360.1257-0.11850.33870.2218-0.05050.22810.0196-0.02340.0055-0.00190.002430.676-28.19162.11
112.7891-0.13771.55080.5541-1.34978.0513-0.202-0.07540.3218-0.03060.1676-0.3103-0.1166-0.27090.03450.0610.03040.06860.0937-0.07280.424426.35122.46720.751
126.8492-1.36554.56920.2755-0.85144.64140.14510.5269-0.102-0.0089-0.09720.04140.3003-0.0443-0.0480.0924-0.01850.15410.14960.05760.4017-19.618-20.6723.396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION2B1 - 255
3X-RAY DIFFRACTION3C1 - 255
4X-RAY DIFFRACTION4D1 - 255
5X-RAY DIFFRACTION5E1 - 255
6X-RAY DIFFRACTION6F1 - 255
7X-RAY DIFFRACTION7U862 - 872
8X-RAY DIFFRACTION8V861 - 873
9X-RAY DIFFRACTION9W861 - 872
10X-RAY DIFFRACTION10X862 - 871
11X-RAY DIFFRACTION11Y861 - 873
12X-RAY DIFFRACTION12Z862 - 872

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