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- PDB-8u0p: Synaptic complex of human DNA polymerase Lambda DL variant engage... -

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Basic information

Entry
Database: PDB / ID: 8u0p
TitleSynaptic complex of human DNA polymerase Lambda DL variant engaged on a noncomplementary DNA double-strand break
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / NONHOMOLOGOUS END-JOINING / BASE EXCISION REPAIR / DNA POLYMERASE / TRANSFERASE / TRANSFERASE-DNA complex
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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / 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 beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily ...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 beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKaminski, A.M. / Pedersen, L.C. / Bebenek, K. / Kunkel, T.A. / Chiruvella, K.K. / Ramsden, D.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA097096 United States
CitationJournal: DNA Repair (Amst) / Year: 2024
Title: DNA polymerase lambda Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining.
Authors: Kaminski, A.M. / Chiruvella, K.K. / Ramsden, D.A. / Bebenek, K. / Kunkel, T.A. / Pedersen, L.C.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: 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 (5'-D(*CP*GP*GP*CP*AP*GP*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)44,93013
Polymers44,1534
Non-polymers7779
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-87 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.205, 60.068, 140.729
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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Protein , 1 types, 1 molecules A

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


Mass: 37794.238 Da / Num. of mol.: 1
Mutation: Glu465-Gln471 deletion and replacement with single glycine
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

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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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Non-polymers , 6 types, 356 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: 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
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 85 mM Na cacodylate pH 6.5, 0.17 M ammonium sulfate, 25.5 % (w/v) PEG 8000, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38985 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.17 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.037 / Rrim(I) all: 0.09 / Rsym value: 0.082 / Net I/σ(I): 19.29
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1913 / CC1/2: 0.69 / CC star: 0.904 / Rpim(I) all: 0.347 / Rrim(I) all: 0.812 / Rsym value: 0.73 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.4 Å / SU ML: 0.198 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.4881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 1935 5.01 %random
Rwork0.1724 36703 --
obs0.1734 38638 97.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 426 40 347 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473111
X-RAY DIFFRACTIONf_angle_d0.7194324
X-RAY DIFFRACTIONf_chiral_restr0.0452482
X-RAY DIFFRACTIONf_plane_restr0.0067472
X-RAY DIFFRACTIONf_dihedral_angle_d11.5341930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.31841080.27732110X-RAY DIFFRACTION80.36
1.93-1.980.2551410.2282583X-RAY DIFFRACTION97.92
1.98-2.040.2271340.20042565X-RAY DIFFRACTION97.09
2.04-2.10.23351490.18392629X-RAY DIFFRACTION98.65
2.1-2.180.21521300.18612622X-RAY DIFFRACTION98.89
2.18-2.260.24081430.19212616X-RAY DIFFRACTION99
2.26-2.370.21831450.17312657X-RAY DIFFRACTION99.43
2.37-2.490.22181360.18092650X-RAY DIFFRACTION99.39
2.49-2.650.19671390.18362683X-RAY DIFFRACTION99.54
2.65-2.850.22041340.18512656X-RAY DIFFRACTION99.11
2.85-3.140.19971370.18042691X-RAY DIFFRACTION99.4
3.14-3.590.18281480.16182694X-RAY DIFFRACTION99.75
3.59-4.530.14011440.13952751X-RAY DIFFRACTION99.79
4.53-39.40.17381470.16382796X-RAY DIFFRACTION96.87
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)
10.752715106671-0.1171519937180.251340844661.571236172820.003913753220211.268983313480.03813859309540.347836244586-0.0107081686077-0.6892944822770.246123910987-0.581522951621-0.3987390977050.325142413746-0.2424633784380.498530906616-0.1046854557770.1448107875140.436812104334-0.04590717459930.400139288363-7.5219761767325.5375319078-26.5771796662
21.25720200956-0.1616350687390.2968445694252.17983850353-0.2374461173091.18358565417-0.0995763288766-0.226656977920.1510236414310.122695833720.13671445481-0.109452719907-0.0729414946312-0.172313173063-0.04197576251040.1616392389720.0115330426338-0.01294795529170.190861115266-0.04193674708510.177993147509-13.891651970620.17975211080.776158867698
31.25354063716-0.4362621551640.462069859581.095041754220.3991110925742.413810095670.124880157776-0.000762492233573-0.3374411595840.08748194450330.0260327806015-0.005246389384470.34889570197-0.0469543522917-0.1486013023680.205856842498-0.0266822454161-0.02394682217960.159458065543-0.003184601051570.258883627777-11.3315809583-5.11671663715-7.77089019614
41.233947407980.2035517076180.6913954627422.106680767790.2801357724141.872397486210.02245362311530.269399846327-0.08617795256-0.3764469571630.02230645837090.02634431610670.03515305931060.0370222537325-0.04506162491010.2461337391130.00204637226141-0.00688143547490.238285375026-0.04764200897020.178641224512-19.23141013581.76509359604-27.8588497057
51.245658165970.308634220853-0.5397911481550.9965084862750.8994595594991.52249441508-0.006431372364740.2149686282360.0585288032823-0.138679808344-0.01030778346840.189422700751-0.0986458063332-0.1823572377250.0363285603260.1630560695610.00970437085139-0.01582888160590.20916575165-0.01164535128640.14603008142-25.338295550915.0589089311-16.6920898528
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 237:329AA237 - 3291 - 93
22chain A and resid 330:386AA330 - 38694 - 150
33chain A and resid 387:495AA387 - 495151 - 253
44chain A and resid 496:575AA496 - 575254 - 322
55chain T or chain P or chain DT - DJ - L1 - 4

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