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- PDB-2od8: Structure of a peptide derived from Cdc9 bound to PCNA -

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Basic information

Entry
Database: PDB / ID: 2od8
TitleStructure of a peptide derived from Cdc9 bound to PCNA
Components
  • DNA ligase I, mitochondrial precursor
  • Proliferating cell nuclear antigen
KeywordsPROTEIN BINDING / homotrimer / PCNA-peptide complex / PCNA
Function / homology
Function and homology information


Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Okazaki fragment processing involved in mitotic DNA replication / DNA ligation involved in DNA repair / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / DNA ligase (ATP) / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA ligase (ATP) activity / E3 ubiquitin ligases ubiquitinate target proteins ...Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Okazaki fragment processing involved in mitotic DNA replication / DNA ligation involved in DNA repair / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / DNA ligase (ATP) / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA ligase (ATP) activity / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / DNA ligation / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / DNA biosynthetic process / leading strand elongation / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / nucleotide-excision repair / base-excision repair / mitotic cell cycle / DNA recombination / chromosome, telomeric region / cell division / DNA repair / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. ...DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase 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 / : / Nucleic acid-binding, OB-fold / Alpha Beta
Similarity search - Domain/homology
DNA ligase 1 / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChapados, B.R. / Tainer, J.A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase.
Authors: Vijayakumar, S. / Chapados, B.R. / Schmidt, K.H. / Kolodner, R.D. / Tainer, J.A. / Tomkinson, A.E.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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
Remark 999SEQUENCE CHAIN B IS THE PEPTIDE SYNTHESIZED BASED ON SEQUENCE OF RESIDUES 32-53 OF CDC9 (UNP P04819) ...SEQUENCE CHAIN B IS THE PEPTIDE SYNTHESIZED BASED ON SEQUENCE OF RESIDUES 32-53 OF CDC9 (UNP P04819) SHOWN IN DBREF.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: DNA ligase I, mitochondrial precursor


Theoretical massNumber of molelcules
Total (without water)31,4012
Polymers31,4012
Non-polymers00
Water32418
1
A: Proliferating cell nuclear antigen
B: DNA ligase I, mitochondrial precursor

A: Proliferating cell nuclear antigen
B: DNA ligase I, mitochondrial precursor

A: Proliferating cell nuclear antigen
B: DNA ligase I, mitochondrial precursor


Theoretical massNumber of molelcules
Total (without water)94,2036
Polymers94,2036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Unit cell
Length a, b, c (Å)139.280, 139.280, 139.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, z, -x and -z, -x, y

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28944.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30 / Plasmid: pT7-PCNA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15873
#2: Protein/peptide DNA ligase I, mitochondrial precursor / CDC9 / Polydeoxyribonucleotide synthase


Mass: 2456.945 Da / Num. of mol.: 1 / Fragment: Residues 32-53 / Source method: obtained synthetically
Details: Peptide synthesized based on Cdc9 sequence (UNP P04819), residues 32-53.
References: UniProt: P04819, DNA ligase (ATP)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.6 M (NH4)2SO4, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2002 / Details: Vertical focusing mirror
RadiationMonochromator: single crystal Si(311) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 11287 / Num. obs: 11287 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 94 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2 / Num. unique all: 1104 / Rsym value: 0.418 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PLQ

1plq


Resolution: 2.8→29.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU B: 43.06 / SU ML: 0.371 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.684 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28527 537 4.8 %RANDOM
Rwork0.24681 ---
obs0.24865 10682 99.75 %-
all-11219 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.318 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 0 18 2113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222127
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9912866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10225.37693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99715404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.664159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021550
X-RAY DIFFRACTIONr_nbd_refined0.160.3877
X-RAY DIFFRACTIONr_nbtor_refined0.3130.51423
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.5111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.56
X-RAY DIFFRACTIONr_mcbond_it0.3381.51362
X-RAY DIFFRACTIONr_mcangle_it0.60722148
X-RAY DIFFRACTIONr_scbond_it0.5253837
X-RAY DIFFRACTIONr_scangle_it0.8794.5718
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 39 -
Rwork0.393 786 -
obs--99.16 %
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)
111.4663-4.127613.98914.77561.256620.0461.2736-0.5391-1.35950.9956-0.8022-2.6504-1.1782.0207-0.47141.17830.34050.05151.06230.01621.173140.58818.26547.49
24.11474.8737-0.89387.74530.61181.60870.1806-0.2079-0.05071.07190.1373-0.15090.78410.153-0.31790.98840.1721-0.20150.53050.05370.4796119.45521.1551.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB35 - 454 - 14
2X-RAY DIFFRACTION2AA1 - 2551 - 255

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