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- PDB-2zvk: Crystal structure of PCNA in complex with DNA polymerase eta fragment -

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Basic information

Entry
Database: PDB / ID: 2zvk
TitleCrystal structure of PCNA in complex with DNA polymerase eta fragment
Components
  • DNA polymerase eta
  • Proliferating cell nuclear antigen
KeywordsTRANSFERASE / DNA replication / PCNA / clamp / translesion synthesis / TLS / DNA polymerase / TLS polymerase / complex / PIP-box / DNA polymerase eta / DNA-binding / Nucleus / Systemic lupus erythematosus / Disease mutation / DNA damage / DNA repair / DNA synthesis / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Phosphoprotein / Schiff base / Xeroderma pigmentosum
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 / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding ...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 / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / DNA polymerase binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / epithelial cell differentiation / liver regeneration / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Termination of translesion DNA synthesis / positive regulation of DNA replication / replication fork / Recognition of DNA damage by PCNA-containing replication complex / nuclear estrogen receptor binding / Translesion Synthesis by POLH / male germ cell nucleus / Dual Incision in GG-NER / HDR through Homologous Recombination (HRR) / receptor tyrosine kinase binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to hydrogen peroxide / cellular response to xenobiotic stimulus / cellular response to UV / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / 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: 2.7 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 / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 eta
B: Proliferating cell nuclear antigen
V: DNA polymerase eta
C: Proliferating cell nuclear antigen
W: DNA polymerase eta


Theoretical massNumber of molelcules
Total (without water)93,9116
Polymers93,9116
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-56.3 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.027, 82.027, 310.443
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: 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 eta


Mass: 2507.949 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.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / pH: 3.6
Details: pH3.6, 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: Oct 19, 2005 / 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: 2.7→50 Å / Num. obs: 27933 / % possible obs: 92.1 % / Observed criterion σ(I): -0.4 / Redundancy: 2.5 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.6 / % possible all: 81.3

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Processing

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

1vym


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.88 / SU B: 33.735 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.776 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28582 1398 5 %RANDOM
Rwork0.21489 ---
obs0.21838 26440 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: 30.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6003 0 0 18 6021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225839
X-RAY DIFFRACTIONr_bond_other_d00.025418
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9817899
X-RAY DIFFRACTIONr_angle_other_deg1.273312563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8745767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.82925.337208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.066151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.6321517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026454
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021076
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_it0.8221.53844
X-RAY DIFFRACTIONr_mcbond_other0.0051.51580
X-RAY DIFFRACTIONr_mcangle_it1.41226149
X-RAY DIFFRACTIONr_scbond_it231995
X-RAY DIFFRACTIONr_scangle_it3.2784.51750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 81 -
Rwork0.3 1634 -
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)
11.53661.0473-0.13773.4729-0.11042.61380.0069-0.1613-0.05420.1526-0.1452-0.2253-0.04420.42780.13820.2183-0.00960.00070.23150.05230.07848.502-0.75465.733
28.2089-0.8976-2.44690.10070.26510.7369-0.04850.0072-0.4842-0.0123-0.0240.0916-0.0308-0.06260.07250.81560.102-0.13220.57410.17060.647929.475-2.60368.406
31.4394-0.3268-1.66491.19460.45645.0110.1099-0.128-0.06560.2387-0.1743-0.0505-0.44580.33410.06430.3111-0.1182-0.05560.15570.05770.143464.89626.45235.582
418.133-6.95659.74697.76724.715919.2919-0.2530.321-0.3877-0.1436-0.21260.5993-0.65330.11810.46560.7473-0.16370.23950.3375-0.16170.320755.75742.21638.143
51.08670.3937-0.56912.7577-1.06392.2555-0.16160.0939-0.20740.03250.0854-0.06410.35130.08120.07620.31330.0102-0.01180.1559-0.01070.112652.888-13.32823.931
62.93066.034-0.741928.2543-8.26173.05310.0181-0.3605-0.12840.76010.1820.2833-0.3045-0.3118-0.20010.1963-0.03890.01560.27250.01230.036643.148-11.2368.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION2U693 - 712
3X-RAY DIFFRACTION3B1 - 254
4X-RAY DIFFRACTION4V701 - 710
5X-RAY DIFFRACTION5C1 - 257
6X-RAY DIFFRACTION6W700 - 710

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