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- PDB-7m0b: Pre-catalytic quaternary complex of DNA Polymerase Lambda with bo... -

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Basic information

Entry
Database: PDB / ID: 7m0b
TitlePre-catalytic quaternary complex of DNA Polymerase Lambda with bound mismatched DSB and incoming dUMPNPP
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*G)-3')
  • DNA (5'-D(*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE / Nonhomologous end-joining / Base Excision Repair
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
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKaminski, A.M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A.
Funding support United States, 2items
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
CitationJournal: Nat Commun / Year: 2022
Title: Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining.
Authors: Kaminski, A.M. / Chiruvella, K.K. / Ramsden, D.A. / Bebenek, K. / Kunkel, T.A. / Pedersen, L.C.
History
DepositionMar 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)45,83917
Polymers44,8815
Non-polymers95812
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-118 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.368, 59.961, 139.406
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: 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)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 4 types, 4 molecules TPDU

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


Mass: 1834.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')


Mass: 1809.217 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)
#5: DNA chain DNA (5'-D(*TP*AP*CP*TP*G)-3')


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 391 molecules

#6: 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
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG8000, 13.5% (v/v) glycerol, 0.2M NDSB-201

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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: Nov 6, 2020
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: 2→50 Å / Num. obs: 32471 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.95 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rsym value: 0.153 / Χ2: 0.905 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1562 / CC1/2: 0.663 / CC star: 0.893 / Rsym value: 0.819 / Χ2: 0.41 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFO

2pfo


Resolution: 2→39.4 Å / SU ML: 0.2006 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1621 5 %random
Rwork0.1705 30780 --
obs0.1721 32401 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.95 Å2
Refinement stepCycle: LAST / Resolution: 2→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 424 50 379 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773173
X-RAY DIFFRACTIONf_angle_d0.93784393
X-RAY DIFFRACTIONf_chiral_restr0.0526486
X-RAY DIFFRACTIONf_plane_restr0.0054487
X-RAY DIFFRACTIONf_dihedral_angle_d12.9932971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.27771190.22452405X-RAY DIFFRACTION94.39
2.06-2.120.30921450.19842519X-RAY DIFFRACTION99.63
2.12-2.20.24221400.19382536X-RAY DIFFRACTION99.81
2.2-2.290.23531320.18672581X-RAY DIFFRACTION99.96
2.29-2.390.21511330.182557X-RAY DIFFRACTION99.81
2.39-2.520.22371310.17732554X-RAY DIFFRACTION99.63
2.52-2.680.21181450.18022573X-RAY DIFFRACTION99.74
2.68-2.880.19141250.1722510X-RAY DIFFRACTION96.98
2.88-3.170.21331330.16892604X-RAY DIFFRACTION99.64
3.17-3.630.18841400.15892586X-RAY DIFFRACTION99.71
3.63-4.570.14121350.14092654X-RAY DIFFRACTION99.5
4.57-39.40.19051430.17212701X-RAY DIFFRACTION97.36
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)
10.396032397114-0.366407772722-0.07824663344241.08723871551-0.2393332824810.5778638213810.08265589141640.04325298355290.0297196952259-0.3177859628050.019470846475-0.164004243769-0.15619820355-0.03889805741260.02644715971440.241000758376-0.01077966268020.07667182518220.1495232424160.00559131599290.145825150031-7.8003512504925.5988585297-26.4141054826
20.2626217775580.231091885788-0.1096625756730.60753955194-0.09832134694160.42541121074-0.0710957858756-0.1048541430260.004677258915250.1463786024650.110299500075-0.0951498030496-0.0190466050664-0.1017342403260.003809566673840.08217522629220.0178686248423-0.007076867497960.115282125055-0.02259677887270.096573385175-13.553541313520.18859067150.909488649974
30.4191425395250.03398484756090.3091415492811.145537991290.05697117229141.012528009510.0385967267527-0.0394727451151-0.04187862558880.02340216690050.02084553565850.05069127709980.101703263976-0.0007861322473650.01965224217350.0936663748821-0.0136976934771-0.01029425205970.0928039493754-0.005989159298020.143700219723-11.9639777531-5.39054049093-7.26709816436
40.423454125436-0.09613513773350.2430757480240.2497059611850.2282852797530.584533032446-0.02617257317510.0998853362559-0.03789363702-0.2124205052760.0562644453338-0.00621822707176-0.00454599405248-0.03535355427490.01544949432540.181956363238-0.00760566621874-0.02151032586840.139385545734-0.03202305058860.108769255787-19.89089690571.77308760441-27.6250291787
50.234070249188-0.141208839915-0.1143233209570.2286073080010.1815653596740.208690316267-0.07433608660690.404535921349-0.167695515003-0.1839634190630.3900744475340.0120323986117-0.160194754026-0.33466252660.06667899249410.1985971448270.0724948088662-0.04816297517280.2320536325010.07951888296230.0820587556583-24.149842148621.6917465285-26.8449917787
60.0856287270058-0.1651619129780.06837335049370.266849673562-0.04830435748090.164296177245-0.1350052931580.07967021202430.02412037980870.06953575428410.1317764309180.004889938064140.184441146841-0.1882849444360.003849294544390.0964806227441-0.02638136616180.03631093485490.163726335245-0.01687934330770.13673254625-25.274976760610.2653408149-7.93758374493
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 236:329AA236 - 3291 - 94
22chain A and resid 330:386AA330 - 38695 - 151
33chain A and resid 387:495AA387 - 495152 - 260
44chain A and resid 496:575AA496 - 575261 - 331
55chain T or chain DT - DB - D1 - 4
66chain U or chain PP - UC - N1 - 5

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