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- PDB-7m0a: Incomplete in crystallo incorporation by DNA Polymerase Lambda bo... -

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Basic information

Entry
Database: PDB / ID: 7m0a
TitleIncomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*CP*T)-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
PYROPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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*CP*T)-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)46,18717
Polymers45,1705
Non-polymers1,01612
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-127 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.768, 59.573, 140.726
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) / 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 , 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*CP*T)-3')


Mass: 2113.410 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 , 8 types, 412 molecules

#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80mM Na cacodylate pH 6.5, 0.16M 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 CYRSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 41774 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rsym value: 0.072 / Χ2: 0.457 / Net I/σ(I): 18.3
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 2071 / CC1/2: 0.75 / CC star: 0.926 / Rsym value: 0.703 / Χ2: 0.334 / % possible all: 98.9

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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: 1.83→43.71 Å / SU ML: 0.2043 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.1618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 2077 4.98 %random
Rwork0.169 39642 --
obs0.1702 41719 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 1.83→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 443 52 400 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633249
X-RAY DIFFRACTIONf_angle_d0.77234520
X-RAY DIFFRACTIONf_chiral_restr0.0465498
X-RAY DIFFRACTIONf_plane_restr0.0056506
X-RAY DIFFRACTIONf_dihedral_angle_d12.2674990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.3251290.26572559X-RAY DIFFRACTION97.11
1.87-1.920.24641330.21712612X-RAY DIFFRACTION99.1
1.92-1.970.23421460.19162573X-RAY DIFFRACTION99.09
1.97-2.030.23881290.18532562X-RAY DIFFRACTION97.01
2.03-2.10.22011510.17622614X-RAY DIFFRACTION99.18
2.1-2.170.22541270.182620X-RAY DIFFRACTION99.35
2.17-2.260.18731380.15582639X-RAY DIFFRACTION99.5
2.26-2.360.20481400.16542625X-RAY DIFFRACTION99.42
2.36-2.480.19041360.16382669X-RAY DIFFRACTION99.68
2.48-2.640.19221460.16972646X-RAY DIFFRACTION99.75
2.64-2.840.21151270.17972640X-RAY DIFFRACTION98.86
2.84-3.130.21161370.17762673X-RAY DIFFRACTION98.84
3.13-3.580.18531480.15722669X-RAY DIFFRACTION99.93
3.58-4.510.15391440.13842743X-RAY DIFFRACTION99.97
4.51-43.710.17261460.17512798X-RAY DIFFRACTION97.48
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)
10.3196945072850.0827735671503-0.1489275181451.12549228975-0.2046408494460.9535398912960.06985351570660.07033353550940.0514948328671-0.2807339494160.0856891864636-0.273367980326-0.2005663015730.1370700271590.1501159092580.227503752641-0.03966061500060.07207161378650.240793274366-0.006041124934120.207351522479-7.6769245964325.4098288968-26.3635688463
20.7317701836660.1631201522110.04546265211360.660065132614-0.1049199773830.53744857444-0.0624380481407-0.1353682499940.04736785455040.04592233405180.1117858231171.22005495155E-5-0.00422891296573-0.1195891010670.01626492919680.1198714239590.01477583780620.001518192009580.133139159833-0.01128768473290.110392811227-14.030049487420.28884595460.661136376409
30.476991528593-0.2384976983150.2202947763520.867235826229-0.1300905027061.815455779190.0428048786794-0.0374865036473-0.1612111336740.04527834890340.02964987775830.08691773480690.1580442836930.04372017006330.01662976969850.14081357543-0.0152868040852-0.01398087247050.1186409153110.002956992435030.19246022831-12.3732876576-5.15707354535-7.48545159367
40.5504665231690.03419097584760.1823156261770.2101249145730.1286672555730.9739113749080.06734219572080.107986548697-0.00677164055927-0.175094705138-0.01826295713460.0301188416804-0.02498275580160.03594958850780.002107903411020.2018719876710.0131674025564-0.03351420472110.170663203617-0.02075489497540.153867491864-19.38791888131.53034600593-28.0148633246
50.165402449332-0.3247817725290.04935605208190.1699686946360.04842796825280.0553415169719-0.0586621819550.150731902078-0.1264577888720.05287244712460.06739452124450.1156494161430.1413351334040.003004247389347.86818740794E-50.123218820995-0.007339188508130.01523276044360.168466586738-0.02319485399890.177635163328-24.65676296119.82608110545-9.80907121073
60.0657946105177-0.161066718647-0.2240389215120.2127658245750.1817979922010.3743663673160.1424834856720.364651078441-0.10070890087-0.13798784795-0.04691482033620.0365923009895-0.211771574696-0.01238372305760.008081799980870.2775997583720.0321070627804-0.03900197854050.2327166109860.04153779270780.170066006773-23.891913419922.990393682-27.9156546639
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 - 330
55chain U or chain PP - UC - E1 - 6
66chain T or chain DT - DB - D1 - 4

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