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- PDB-8v1v: Human DNA Ligase I F872L bound to adenylated nicked DNA -

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Basic information

Entry
Database: PDB / ID: 8v1v
TitleHuman DNA Ligase I F872L bound to adenylated nicked DNA
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*(OHU)P*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
  • DNA ligase 1
KeywordsLIGASE/DNA / ADENYLATION DOMAIN / METALLOENZYME / LIGASE / LIGASE-DNA COMPLEX / DNA BINDING PROTEIN
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / 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 / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / 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) / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / PCNA-Dependent Long Patch Base Excision Repair / 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 / DNA repair / intracellular membrane-bounded organelle / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / 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
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: To Be Published
Title: Human DNA Ligase I F872L bound to adenylated nicked DNA
Authors: Tumbale, P.P. / Williams, R.S.
History
DepositionNov 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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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(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
D: DNA (5'-D(*GP*TP*CP*CP*GP*AP*(OHU)P*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,04211
Polymers83,0054
Non-polymers1,0377
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-57 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.966, 96.582, 114.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: 71998.281 Da / Num. of mol.: 1 / Mutation: F872L
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(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')


Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*TP*CP*CP*GP*AP*(OHU)P*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5503.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 244 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MES pH5.5 100mM, Lithium acetate 500mM, PEG 3350 10%

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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: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 35438 / % possible obs: 96.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 36.36 Å2 / Rrim(I) all: 0.218 / Net I/σ(I): 12.75
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.4 % / Num. unique obs: 1750 / Rrim(I) all: 0.941 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.87 Å / SU ML: 0.2781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 1992 5.64 %
Rwork0.1788 33301 -
obs0.1814 35293 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 733 59 237 5926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655888
X-RAY DIFFRACTIONf_angle_d0.64958150
X-RAY DIFFRACTIONf_chiral_restr0.0394929
X-RAY DIFFRACTIONf_plane_restr0.0036926
X-RAY DIFFRACTIONf_dihedral_angle_d16.19472230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.31991400.24782338X-RAY DIFFRACTION96.72
2.36-2.420.33371420.2362373X-RAY DIFFRACTION96.55
2.42-2.490.2621290.22732135X-RAY DIFFRACTION88.06
2.49-2.570.29221430.21272388X-RAY DIFFRACTION97.5
2.57-2.660.27981420.20782374X-RAY DIFFRACTION97.94
2.66-2.770.25021450.2012422X-RAY DIFFRACTION98.47
2.77-2.90.25361420.19262402X-RAY DIFFRACTION98.22
2.9-3.050.27251460.18292426X-RAY DIFFRACTION98.47
3.05-3.240.21771420.17872396X-RAY DIFFRACTION97.43
3.24-3.490.23181430.17282383X-RAY DIFFRACTION95.57
3.49-3.840.20671340.15172259X-RAY DIFFRACTION91.27
3.84-4.40.17981470.14782435X-RAY DIFFRACTION97.25
4.4-5.540.18751450.15972438X-RAY DIFFRACTION96.63
5.54-40.870.19571520.18482532X-RAY DIFFRACTION95.45
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)
11.64253155845-0.119988837087-1.482463654580.9811031813820.401428971662.921212396430.0719151871963-0.1613232853290.1380402587890.0931903698294-0.062720980755-0.00101629736899-0.1474186873270.0123740467117-0.0133486632910.237930731746-0.0280931003331-0.01510069067150.2418225908360.00372442845250.26596788895735.76998457288.29242572786-6.63156768624
20.6957043948460.2032939455260.002095906930530.7344251420070.05000439214690.4545244284470.01753490332270.0231666471099-0.0705999158242-0.00566859633134-0.01761184099770.0555562901066-0.0261990119716-0.0362937319810.0033135880440.2862016473930.03542702895370.01120624009680.2123466366870.004241469913190.23482314142221.9800013536-19.0552073127-18.1846501272
32.3044892175-0.162163788674-0.5285224824511.628392831460.5895460566571.83483789320.0985753857426-0.04329458714020.007910571316210.0200373434336-0.11630585740.1256648559320.139777681158-0.2439350191730.02286566227630.273320873004-0.00354224292346-0.02402988872960.2708479971910.006850028420640.281773610321-1.361238906144.17422149507-5.47386389263
41.297105328110.008417341613452.809986732470.292981341893-0.3833057018546.599670200170.00285717504515-0.1874602504210.02930949847270.2507641686540.165465245510.00340759755994-0.402841983894-0.390374354249-0.1524243161530.365472134204-0.007501961458410.03949089627160.332547786902-0.02809405343950.26562331870815.9981376326-5.421829310068.1296175124
53.673649725130.517848430902-1.026212166951.504302526570.2400617526722.742124122750.01684261599710.3123654977630.2240482412590.06079006545950.1678370796640.201570745080.0881494035582-0.0762523254845-0.1814359513820.3443450053790.01164141965830.006448737783090.344769493174-0.003253954925840.28111640315713.57833173833.23206304707-20.0423288427
64.693040485971.90799554062-3.718405733723.91186055509-3.093722998313.605696269140.1502390331890.1098885372080.08038734146070.03297428592020.1118652294490.1479206409860.1360479412550.155463299259-0.2470640972180.2446372972550.0143990650368-0.03168937945590.262114832122-0.0145171373860.24201514144415.1892965376-0.427389001417-12.241181827
73.666322934360.7329560702130.6777253645850.492190195328-0.4678318958384.237815118250.251647185706-0.4339521555650.07511314900020.225397296565-0.0603891994847-0.231839823826-0.4100225746160.0725083049106-0.1832169967490.4399993787540.0194206181054-0.007851601136750.396374035194-0.01331059813150.24575248987319.4120505423-5.0258209046814.4451376773
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 258 through 469 )AA258 - 4691 - 212
22chain 'A' and (resid 470 through 741 )AA470 - 741213 - 484
33chain 'A' and (resid 742 through 902 )AA742 - 902485 - 645
44chain 'B' and (resid 3 through 13 )BG3 - 13
55chain 'C' and (resid 1 through 7 )CH1 - 7
66chain 'D' and (resid 9 through 19 )DJ9 - 19
77chain 'D' and (resid 20 through 26 )DJ20 - 26

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