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- PDB-9npu: Pre-catalytic ternary complex of DNA Polymerase Lambda with bound... -

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Basic information

Entry
Database: PDB / ID: 9npu
TitlePre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate containing template ribonucleotide opposite primer terminus, and incoming dUMPNPP
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
  • DNA/RNA (5'-D(*CP*GP*GP*CP*A)-R(P*G)-D(P*TP*AP*CP*TP*G)-3')
KeywordsTRANSFERASE / Family X polymerase / nonhomologous end joining
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site ...DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsKaminski, A.M. / Luthman, A.J. / Pedersen, L.C. / Ramsden, D.A. / Kunkel, T.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102645 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA097096 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
CitationJournal: Nat Commun / Year: 2025
Title: Nonhomologous end-joining uses distinct mechanisms to repair each strand of a double strand break.
Authors: Luthman, A.J. / Chiruvella, K.K. / Kaminski, A.M. / Kunkel, T.A. / Pedersen, L.C. / Ramsden, D.A.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: 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 polymerase lambda
T: DNA/RNA (5'-D(*CP*GP*GP*CP*A)-R(P*G)-D(P*TP*AP*CP*TP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,78512
Polymers44,9264
Non-polymers8588
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-77 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.204, 59.923, 140.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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DNA chain , 2 types, 2 molecules PD

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


Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AT

#1: Protein DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 38550.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: DNA/RNA hybrid DNA/RNA (5'-D(*CP*GP*GP*CP*A)-R(P*G)-D(P*TP*AP*CP*TP*G)-3')


Mass: 3390.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 273 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 68 mM Na cacodylate pH 6.5, 20.4% (w/v) PEG8000, 136 mM ammonium sulfate, 12% (v/v) glycerol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2025
RadiationMonochromator: DOUBLE CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.63→41.01 Å / Num. obs: 60232 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 19.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.035 / Rrim(I) all: 0.116 / Net I/σ(I): 11
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.541 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5928 / CC1/2: 0.407 / Rpim(I) all: 0.526 / Rrim(I) all: 1.631 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→40.99 Å / SU ML: 0.1924 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 3029 5.03 %random
Rwork0.1781 57196 --
obs0.1792 60225 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.75 Å2
Refinement stepCycle: LAST / Resolution: 1.63→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 427 48 265 3203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01173112
X-RAY DIFFRACTIONf_angle_d1.08264322
X-RAY DIFFRACTIONf_chiral_restr0.0613479
X-RAY DIFFRACTIONf_plane_restr0.0109480
X-RAY DIFFRACTIONf_dihedral_angle_d12.9685932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.37551450.32342571X-RAY DIFFRACTION100
1.65-1.680.3081390.29682543X-RAY DIFFRACTION99.89
1.68-1.710.2961300.27262602X-RAY DIFFRACTION100
1.71-1.740.2551600.25352511X-RAY DIFFRACTION100
1.74-1.770.26491140.23722591X-RAY DIFFRACTION100
1.77-1.810.27441340.23392572X-RAY DIFFRACTION100
1.81-1.850.23691350.22012560X-RAY DIFFRACTION100
1.85-1.890.23571370.20292578X-RAY DIFFRACTION100
1.89-1.940.22191510.20282570X-RAY DIFFRACTION99.96
1.94-1.990.20561260.18362567X-RAY DIFFRACTION100
1.99-2.050.19591290.18022588X-RAY DIFFRACTION100
2.05-2.120.2091460.17632573X-RAY DIFFRACTION100
2.12-2.190.20861360.17582588X-RAY DIFFRACTION100
2.19-2.280.21171360.17232591X-RAY DIFFRACTION100
2.28-2.380.21061340.16592592X-RAY DIFFRACTION100
2.38-2.510.17071340.16362608X-RAY DIFFRACTION99.93
2.51-2.670.18421460.16562610X-RAY DIFFRACTION99.96
2.67-2.870.22991260.17982618X-RAY DIFFRACTION100
2.87-3.160.18511440.16342642X-RAY DIFFRACTION100
3.16-3.620.18041410.15392621X-RAY DIFFRACTION99.96
3.62-4.560.14611390.14112693X-RAY DIFFRACTION100
4.56-40.990.19191470.18262807X-RAY DIFFRACTION99.86
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)
10.612300775739-0.07101836017740.05134512795641.801893718230.07827602939060.969296724023-0.02933782342640.5040805828330.0393169954847-0.6145175898090.355877129789-0.606748360836-0.3695628842090.5205216396240.002355991533440.508937957153-0.1308443269930.1458049459860.573206000129-0.061424951750.427429505068-7.57125.922-25.877
21.858045674470.246311288291-0.0299820943231.880772128340.05397015861721.21156718294-0.0551916403552-0.2470155578650.1702641369040.06453407051810.106877990215-0.0342059336997-0.0397853203142-0.09824755852973.84469520070.1337970803260.00173072414737-0.008561360791070.14324598547-0.03533579081750.137238673964-13.73520.2940.76
31.33646597751-0.4816910936410.6935759544761.13150888962-0.161748397232.246346196750.114521310578-0.0662720548861-0.4539779910170.03998075913720.02441871012250.005391281211940.292757216076-0.003352516771090.01895174790360.179533982826-0.0217938583683-0.01999764080090.118085768468-0.0209055208850.250333004743-12.448-5.078-7.455
41.00576550932-0.6500479472940.3522825351181.856600713610.06119014254692.321495277130.07646830274450.49291186536-0.0592268163785-0.400128244889-0.01954773589320.0911146769336-0.06390487009110.1073087320340.006855754279490.2673477637990.00222650197501-0.01479451263150.288586057492-0.06320107647640.18020150027-19.6841.878-27.729
51.607770231420.17772626428-0.1925085108160.5795377704370.8065053539471.191128615610.005800741375340.2693291883520.10512310812-0.1838118319120.02396633603840.164135196473-0.175193300169-0.171171023435-0.002216398931740.1745317512060.0145560429382-0.01012323389210.162171569227-0.003306843094370.144225585345-24.71215.534-16.993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 239:329 )A239 - 329
2X-RAY DIFFRACTION2( CHAIN A AND RESID 330:386 )A330 - 386
3X-RAY DIFFRACTION3( CHAIN A AND RESID 387:495 )A387 - 495
4X-RAY DIFFRACTION4( CHAIN A AND RESID 496:575 )A496 - 575
5X-RAY DIFFRACTION5( CHAIN T AND RESID 1:11 ) OR ( CHAIN P AND RESID 1:6 ) OR ( CHAIN D AND RESID 1:4 )T1 - 11
6X-RAY DIFFRACTION5( CHAIN T AND RESID 1:11 ) OR ( CHAIN P AND RESID 1:6 ) OR ( CHAIN D AND RESID 1:4 )P1 - 6
7X-RAY DIFFRACTION5( CHAIN T AND RESID 1:11 ) OR ( CHAIN P AND RESID 1:6 ) OR ( CHAIN D AND RESID 1:4 )D1 - 4

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