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- PDB-3qvg: XRCC1 bound to DNA ligase -

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Basic information

Entry
Database: PDB / ID: 3qvg
TitleXRCC1 bound to DNA ligase
Components
  • DNA ligase 3
  • DNA repair protein XRCC1
KeywordsDNA BINDING PROTEIN/LIGASE / BRCT domain / DNA repair / XRCC1 / DNA ligase III-alpha / DNA BINDING PROTEIN-LIGASE complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / HDR through MMEJ (alt-NHEJ) / DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, DNA ligation ...Resolution of AP sites via the single-nucleotide replacement pathway / HDR through MMEJ (alt-NHEJ) / DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, DNA ligation / ADP-D-ribose modification-dependent protein binding / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of protein ADP-ribosylation / DNA ligase activity / poly-ADP-D-ribose binding / DNA ligase (ATP) / positive regulation of single strand break repair / DNA ligase (ATP) activity / voluntary musculoskeletal movement / replication-born double-strand break repair via sister chromatid exchange / cerebellum morphogenesis / single strand break repair / DNA ligation / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / response to hydroperoxide / mitochondrial DNA repair / Resolution of AP sites via the single-nucleotide replacement pathway / DNA biosynthetic process / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / base-excision repair, gap-filling / mitochondrion organization / Gap-filling DNA repair synthesis and ligation in GG-NER / response to organic substance / hippocampus development / double-strand break repair via homologous recombination / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / chromosome, telomeric region / response to hypoxia / response to xenobiotic stimulus / cell cycle / cell division / DNA repair / chromatin / nucleolus / enzyme binding / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / 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. ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / 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. / BRCT domain / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Nucleic acid-binding, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA ligase 3 / DNA repair protein XRCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsCuneo, M.J. / Krahn, J.M. / London, R.E.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The structural basis for partitioning of the XRCC1/DNA ligase III-{alpha} BRCT-mediated dimer complexes.
Authors: Cuneo, M.J. / Gabel, S.A. / Krahn, J.M. / Ricker, M.A. / London, R.E.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 8, 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 13, 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: DNA ligase 3
B: DNA repair protein XRCC1
C: DNA ligase 3
D: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)45,4854
Polymers45,4854
Non-polymers00
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-15 kcal/mol
Surface area19340 Å2
MethodPISA
2
A: DNA ligase 3
B: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)22,7432
Polymers22,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-3 kcal/mol
Surface area10460 Å2
MethodPISA
3
C: DNA ligase 3
D: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)22,7432
Polymers22,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-3 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.140, 61.470, 163.670
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 DNA ligase 3 / / DNA ligase III / Polydeoxyribonucleotide synthase [ATP] 3


Mass: 10113.484 Da / Num. of mol.: 2 / Fragment: unp residues 924-1008
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG3 / Plasmid: pCola-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: P49916, DNA ligase (ATP)
#2: Protein DNA repair protein XRCC1 / / X-ray repair cross-complementing protein 1


Mass: 12629.252 Da / Num. of mol.: 2 / Fragment: unp residues 531-631
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xrcc-1, Xrcc1 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q60596
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG4000, 0.1 M Tris, 0.2 M NaAcetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jan 25, 2011
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→35 Å / Num. all: 18358 / Num. obs: 18358 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Χ2: 1.322 / Net I/σ(I): 20.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.26-2.343.30.26114643.175180.4
2.34-2.436.70.18818351.766199.9
2.43-2.556.80.16118741.5151100
2.55-2.686.80.13418361.4771100
2.68-2.856.80.1118411.4011100
2.85-3.076.80.08418751.2191100
3.07-3.386.70.06618641.1211100
3.38-3.865.80.06618581.188197.3
3.86-4.876.20.04818700.897197.1
4.87-356.40.05620410.705199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 3PC7, 3PC6

3pc7

3pc6


Resolution: 2.26→34.061 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7963 / SU ML: 0.28 / σ(F): 0 / σ(I): 0 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 889 5.13 %random
Rwork0.1987 ---
obs0.2023 17331 92.24 %-
all-17331 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.083 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 106.99 Å2 / Biso mean: 29.9829 Å2 / Biso min: 6.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.8599 Å20 Å20 Å2
2--3.3136 Å20 Å2
3----4.1736 Å2
Refinement stepCycle: LAST / Resolution: 2.26→34.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 0 297 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033166
X-RAY DIFFRACTIONf_angle_d0.6044337
X-RAY DIFFRACTIONf_chiral_restr0.045451
X-RAY DIFFRACTIONf_plane_restr0.002586
X-RAY DIFFRACTIONf_dihedral_angle_d10.7121173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2602-2.40180.39271160.2962058217471
2.4018-2.58710.32821600.23412775293596
2.5871-2.84740.28061400.20742827296797
2.8474-3.25910.2651500.21042899304998
3.2591-4.1050.27211720.19672747291992
4.105-34.06520.21181510.15913136328799
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)
13.14891.02560.40493.4795-0.46513.02170.0501-0.15360.08510.13060.02520.1859-0.0055-0.1018-0.00010.06450.01130.00540.03650.00340.0833-6.76728.999113.5796
20.466-0.337-0.22950.47550.19030.1256-0.0486-0.4716-0.1236-0.59440.16780.6588-0.1970.1418-0.00030.1283-0.068-0.06360.21360.03460.23189.319412.72212.8657
31.81831.0810.71091.32660.69664.21720.09370.079-0.04820.04620.0290.08750.3229-0.002600.16380.0479-0.00420.0573-0.00110.1355-9.47170.1714-9.2758
41.3076-0.0321-0.6563.4863-0.11952.47850.03330.016-0.2196-0.0794-0.06990.19450.1466-0.1183-0.00010.0580.0031-0.00780.12620.01950.1163-8.6533-7.867324.8252
50.83040.88-0.14711.4162-0.46330.3358-0.34530.22690.4341-1.35580.9070.0805-0.06110.1113-0.00640.38170.20450.08180.58450.2310.36819.0641-7.743323.4994
61.6961-0.4334-1.25350.85080.02165.9361-0.01710.0635-0.01980.01910.03380.1303-0.1853-0.3321-00.1672-0.0135-0.00920.1108-0.00340.1293-10.7896-0.501748.5841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not resname HOHA0
2X-RAY DIFFRACTION2chain B and resid 528:536 and not resname HOHB0
3X-RAY DIFFRACTION3chain B and resid 537:631 and not resname HOHB0
4X-RAY DIFFRACTION4chain C and not resname HOHC0
5X-RAY DIFFRACTION5chain D and resid 528:536 and not resname HOHD0
6X-RAY DIFFRACTION6chain D and resid 537:631 and not resname HOHD0

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