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- PDB-7m09: Pre-catalytic quaternary complex of DNA Polymerase Lambda with bl... -

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Basic information

Entry
Database: PDB / ID: 7m09
TitlePre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate and incoming dUMPNPP
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*A)-3')
  • DNA (5'-D(*GP*CP*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: 1.65 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*A)-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(*GP*CP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,74616
Polymers44,8665
Non-polymers88011
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-107 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.941, 59.615, 140.042
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*A)-3')


Mass: 1505.025 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(*GP*CP*AP*CP*TP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 453 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80mM Na cacodylate pH 6.5, 0.16mM calcium acetate, 14.4% (w/v) PEG 8000, 20% (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 25, 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: 1.65→50 Å / Num. obs: 57424 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.54 Å2 / CC1/2: 1 / CC star: 1 / Rsym value: 0.067 / Χ2: 0.523 / Net I/σ(I): 20.57
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 2805 / CC1/2: 0.75 / CC star: 0.926 / Rsym value: 0.803 / Χ2: 0.36 / % possible all: 99.9

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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: 1.65→39.17 Å / SU ML: 0.1766 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2870 5 %random
Rwork0.1677 54476 --
obs0.1687 57346 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 423 48 442 3432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013195
X-RAY DIFFRACTIONf_angle_d1.03514430
X-RAY DIFFRACTIONf_chiral_restr0.0606491
X-RAY DIFFRACTIONf_plane_restr0.0084500
X-RAY DIFFRACTIONf_dihedral_angle_d12.303984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.26741360.2472416X-RAY DIFFRACTION95.33
1.67-1.70.24911200.21372614X-RAY DIFFRACTION99.82
1.7-1.730.22141630.20542519X-RAY DIFFRACTION99.89
1.73-1.770.2161170.20042562X-RAY DIFFRACTION99.81
1.77-1.80.29291300.24882589X-RAY DIFFRACTION99.67
1.8-1.840.25881360.20352546X-RAY DIFFRACTION99.74
1.84-1.880.25321410.18572580X-RAY DIFFRACTION99.78
1.88-1.930.18581410.17252581X-RAY DIFFRACTION99.74
1.93-1.980.17811340.16522563X-RAY DIFFRACTION99.89
1.98-2.040.19041280.1632580X-RAY DIFFRACTION99.67
2.04-2.110.20191470.16952572X-RAY DIFFRACTION100
2.11-2.180.20131310.17272595X-RAY DIFFRACTION100
2.18-2.270.19911390.16882597X-RAY DIFFRACTION99.93
2.27-2.370.19171380.16492586X-RAY DIFFRACTION99.82
2.37-2.50.18531290.16562601X-RAY DIFFRACTION99.71
2.5-2.660.18591460.16172600X-RAY DIFFRACTION99.6
2.66-2.860.17481260.16652606X-RAY DIFFRACTION99.27
2.86-3.150.18391420.16882643X-RAY DIFFRACTION99.96
3.15-3.60.18161400.14892629X-RAY DIFFRACTION99.89
3.6-4.540.1491410.13882696X-RAY DIFFRACTION100
4.54-39.170.16061450.17282801X-RAY DIFFRACTION99.53
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)
10.26820016026-0.110963532462-0.08558115487570.949920670634-0.1923666748330.7221502228890.08900509141920.155876662781-0.00308845244007-0.3803454775150.138465209732-0.322745081916-0.1657694704380.2325060264090.1076992491760.287962650615-0.05231947303210.09049368258010.308343282131-0.03042482592790.238202926658-7.7958898432425.6396442576-25.9119091284
20.611516315667-0.01523265445960.06742792692870.473537457672-0.1952051587750.468709575763-0.0763172156551-0.1283059934770.07674567348010.05427565912020.0966139776542-0.045158056409-0.0157455628585-0.1276885641240.009734143248720.1203187010530.00928074406775-0.006501827444080.122609188962-0.02206224348790.124463695495-13.822608896220.11507239990.722643749167
30.559642817774-0.1197414009050.2822604896490.573608640453-0.1858771596791.337034114910.04815875315790.0036185437219-0.1654463579780.03004538933420.0246112447130.03828080947810.1548543917140.09842323717480.008977940432920.136494388673-0.00151778249571-0.01445125075680.102208762229-0.009300660360460.174492028592-12.3491535422-5.18604575328-7.54419148634
40.418825808045-0.0565084326180.3261688616380.3462304786250.1961962083870.9264781680440.0008756273389850.169427547402-0.0329703356406-0.2323584597050.002294848368650.0493970420523-0.06643567362810.08885255640240.02122708464250.2063952918840.0116139791237-0.03669635352710.181470243096-0.02351662546520.142648702592-19.81488107491.74380164259-27.8373707531
50.231473689512-0.3599680612670.11041787340.2635912851940.03118033013530.0359559741935-0.02496096300050.0865263335195-0.01005261095040.0589742936192-0.002407401752120.1426006126050.0336439046824-0.0485345990851-7.92216639365E-70.135050379786-0.007506542833280.01357536364670.164245218563-0.02551350618760.185419831774-26.11702898910.2232019006-9.0026634427
60.118399384221-0.0869453436471-0.2131333649660.05485041519290.1208468818830.3322407556250.1346310257960.22486528772-0.00279820582265-0.132621012898-0.01331045703610.0501289595486-0.136696293491-0.08351362835560.06289057888460.2470926305540.0344491129735-0.04382240433290.2350663269540.03503069639430.156740308971-23.863374930823.0957653759-27.7462432459
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 238:329AA238 - 3293 - 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 U or chain PP - UC - E1 - 6
66chain T or chain DT - DB - D1 - 4

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