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- PDB-7kr3: Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate -

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Basic information

Entry
Database: PDB / ID: 7kr3
TitleHuman DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate
Components
  • DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3')
  • DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3')
  • DNA ligase 1
KeywordsLIGASE/DNA / DNA ligase / DNA replication / DNA repair / Replication / fidelity / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mismatch repair / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA recombination / cell division / intracellular membrane-bounded organelle / DNA repair / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding
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 ...: / 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.778 Å
AuthorsTumbale, P.P. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nat Commun / Year: 2021
Title: High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication.
Authors: Williams, J.S. / Tumbale, P.P. / Arana, M.E. / Rana, J.A. / Williams, R.S. / Kunkel, T.A.
History
DepositionNov 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase 1
B: DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3')
C: DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5996
Polymers83,1934
Non-polymers4062
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-54 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.681, 101.665, 115.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA ligase 1 / DNA ligase I / Polydeoxyribonucleotide synthase [ATP] 1


Mass: 71916.227 Da / Num. of mol.: 1 / Mutation: E346A, E592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18858, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules BCD

#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3')


Mass: 3598.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3')


Mass: 2088.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: DNA chain DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3')


Mass: 5589.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 3 types, 19 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 150 mM lithium acetate, 10% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.778→50 Å / Num. obs: 21959 / % possible obs: 97.5 % / Redundancy: 6 % / Rsym value: 0.066 / Net I/σ(I): 21.53
Reflection shellResolution: 2.778→2.85 Å / Num. unique obs: 1097 / CC1/2: 0.924 / Rsym value: 0.422

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P09

6p09


Resolution: 2.778→36.84 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1998 9.14 %
Rwork0.1932 19868 -
obs0.1974 21866 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.2 Å2 / Biso mean: 87.7862 Å2 / Biso min: 43.84 Å2
Refinement stepCycle: final / Resolution: 2.778→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 750 42 17 5738
Biso mean--72.93 73.09 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025901
X-RAY DIFFRACTIONf_angle_d0.5088149
X-RAY DIFFRACTIONf_chiral_restr0.035916
X-RAY DIFFRACTIONf_plane_restr0.003928
X-RAY DIFFRACTIONf_dihedral_angle_d16.5943463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7782-2.84760.35991400.3101140196
2.8476-2.92460.34991410.2951138898
2.9246-3.01060.38721410.2867141299
3.0106-3.10770.30781450.2682143599
3.1077-3.21880.33361430.2361140898
3.2188-3.34760.28021410.2154139497
3.3476-3.49980.27281440.2047143999
3.4998-3.68410.28031440.205142899
3.6841-3.91470.2371430.1956142498
3.9147-4.21660.21761410.1811140797
4.2166-4.64020.20041420.1565141395
4.6402-5.30990.21111430.1626142496
5.3099-6.68340.2451470.1931147098
6.6834-36.840.18351430.1672142590
Refinement TLS params.Method: refined / Origin x: 19.7658 Å / Origin y: -4.302 Å / Origin z: -10.6125 Å
111213212223313233
T0.5948 Å20.0428 Å20.0061 Å2-0.7289 Å20.02 Å2--0.3051 Å2
L1.3036 °20.2297 °2-0.187 °2-1.3255 °20.0903 °2--1.3974 °2
S0.1038 Å °-0.1219 Å °0.0779 Å °0.0507 Å °-0.0907 Å °0.0574 Å °-0.0653 Å °0.1547 Å °-0.0188 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA262 - 901
2X-RAY DIFFRACTION1allB3 - 14
3X-RAY DIFFRACTION1allC1 - 7
4X-RAY DIFFRACTION1allD9 - 26
5X-RAY DIFFRACTION1allD101
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allS2 - 49

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