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- PDB-3k4x: Eukaryotic Sliding Clamp PCNA Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3k4x
TitleEukaryotic Sliding Clamp PCNA Bound to DNA
Components
  • DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')
  • DNA (5'-D(*TP*TP*TP*TP*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN/DNA / DNA replication / DNA-binding / clamp loader / DNA sliding clamp / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / E3 ubiquitin ligases ubiquitinate target proteins / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 ...positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / E3 ubiquitin ligases ubiquitinate target proteins / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / Termination of translesion DNA synthesis / PCNA complex / lagging strand elongation / DNA damage tolerance / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / Dual incision in TC-NER / translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / 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
DNA / DNA (> 10) / Proliferating cell nuclear antigen / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsMcNally, R. / Kuriyan, J.
CitationJournal: Bmc Struct.Biol. / Year: 2010
Title: Analysis of the role of PCNA-DNA contacts during clamp loading.
Authors: McNally, R. / Bowman, G.D. / Goedken, E.R. / O'Donnell, M. / Kuriyan, J.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')
C: DNA (5'-D(*TP*TP*TP*TP*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)96,0713
Polymers96,0713
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.935, 93.712, 136.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 88764.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: POL30, YBR088C, YBR0811 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15873, UniProt: A6ZL36*PLUS
#2: DNA chain DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')


Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*TP*TP*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')


Mass: 4325.825 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsCHAIN A CONSISTS OF THREE IDENTICAL SUBUNITS CONNECTED BY TWO LINKERS. THE MUTATIONS R110S, Y114S ...CHAIN A CONSISTS OF THREE IDENTICAL SUBUNITS CONNECTED BY TWO LINKERS. THE MUTATIONS R110S, Y114S OCCUR IN ONE SUBUNIT ONLY AS PER THE AUTHORS, IT WAS NOT POSSIBLE TO IDENTIFY THE ORDER OF THE SUBUNITS IN THE STRUCTURE BECAUSE THE ELECTRON DENSITY MAP DID NOT DISTINGUISH THE POSITIONS OF THE MUTATIONS AND BECAUSE THE LINKERS ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP. SINCE IT IS UNKNOWN WHICH SUBUNIT IN THE STRUCTURE CONTAINS THE MUTATIONS, THE RESIDUES AT THESE POSITIONS IN ALL THREE SUBUNITS WERE BUILT AS WILD-TYPE

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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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Na Acetate, 100 mM NaCl, 14% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. all: 22549 / Num. obs: 22002 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.148 / Χ2: 1.144 / Net I/σ(I): 10.7
Reflection shellResolution: 2.98→3.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1957 / Χ2: 0.942 / % possible all: 88.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.4_162refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PLQ

1plq


Resolution: 2.98→46.856 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.89 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1121 5.09 %Random
Rwork0.223 ---
obs0.226 22002 97.6 %-
all-22549 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.997 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso max: 447.84 Å2 / Biso mean: 70.198 Å2 / Biso min: 5.04 Å2
Baniso -1Baniso -2Baniso -3
1-6.156 Å20 Å20 Å2
2---3.034 Å2-0 Å2
3----3.122 Å2
Refinement stepCycle: LAST / Resolution: 2.98→46.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5947 407 0 0 6354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036489
X-RAY DIFFRACTIONf_angle_d0.6678837
X-RAY DIFFRACTIONf_chiral_restr0.0391043
X-RAY DIFFRACTIONf_plane_restr0.0021062
X-RAY DIFFRACTIONf_dihedral_angle_d15.4982451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.1230.3521300.2892285241587
3.123-3.2870.371420.2792579272199
3.287-3.4930.3161440.23926512795100
3.493-3.7630.3171380.21926242762100
3.763-4.1410.2491450.20626392784100
4.141-4.740.2451180.1622680279899
4.74-5.970.2181460.192671281799
5.97-46.8620.2571580.2352752291098
Refinement TLS params.Method: refined / Origin x: -31.2819 Å / Origin y: -24.052 Å / Origin z: 30.8908 Å
111213212223313233
T0.9755 Å20.2604 Å2-0.1703 Å2-1.6475 Å2-0.5156 Å2--3.053 Å2
L3.6385 °2-3.2993 °2-5.2494 °2-3.2259 °24.6547 °2--7.5059 °2
S1.168 Å °2.5458 Å °-3.2112 Å °1.5178 Å °-2.3541 Å °-1.5531 Å °0.6142 Å °-2.3518 Å °0.2287 Å °

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