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- PDB-7m0d: Pre-catalytic quaternary complex of DNA Polymerase Lambda with bo... -

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Basic information

Entry
Database: PDB / ID: 7m0d
TitlePre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP
Components
  • DNA (5'-D(*AP*CP*TP*G)-3')
  • DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-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
CITRIC ACID / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / FORMIC ACID / : / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
G: DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3')
F: DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
H: DNA (5'-D(P*GP*CP*CP*G)-3')
B: DNA polymerase lambda
K: DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3')
J: DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
L: DNA (5'-D(P*GP*CP*CP*G)-3')
I: DNA (5'-D(*AP*CP*TP*G)-3')
E: DNA (5'-D(*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,56242
Polymers89,73210
Non-polymers2,82932
Water19,3841076
1
A: DNA polymerase lambda
G: DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3')
F: DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
H: DNA (5'-D(P*GP*CP*CP*G)-3')
E: DNA (5'-D(*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,26820
Polymers44,8665
Non-polymers1,40115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase lambda
K: DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3')
J: DNA (5'-D(*CP*AP*GP*TP*GP*C)-3')
L: DNA (5'-D(P*GP*CP*CP*G)-3')
I: DNA (5'-D(*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,29422
Polymers44,8665
Non-polymers1,42817
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.442, 151.989, 86.473
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38550.961 Da / Num. of mol.: 2
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, 8 molecules GKFJHLIE

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


Mass: 2123.412 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*AP*CP*TP*G)-3')


Mass: 1190.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 10 types, 1108 molecules

#6: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#10: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#11: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#14: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.192M tri-potassium citrate, 18.8% (w/v) PEG 3350

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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: Oct 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: 1.8→50 Å / Num. obs: 115616 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.04 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rsym value: 0.102 / Χ2: 0.578 / Net I/σ(I): 17.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 5755 / CC1/2: 0.859 / CC star: 0.961 / Rsym value: 0.927 / Χ2: 0.364 / % possible all: 100

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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: 1.8→41.78 Å / SU ML: 0.1809 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 4939 4.28 %random
Rwork0.1643 110517 --
obs0.1654 115456 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 846 166 1076 7368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00936558
X-RAY DIFFRACTIONf_angle_d1.03339039
X-RAY DIFFRACTIONf_chiral_restr0.0568983
X-RAY DIFFRACTIONf_plane_restr0.00741019
X-RAY DIFFRACTIONf_dihedral_angle_d12.92431012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.30131520.23913393X-RAY DIFFRACTION92.97
1.82-1.840.22991660.21873703X-RAY DIFFRACTION99.9
1.84-1.860.24261640.21273674X-RAY DIFFRACTION99.95
1.86-1.890.25461640.20763671X-RAY DIFFRACTION99.87
1.89-1.910.24981610.22923556X-RAY DIFFRACTION96.62
1.91-1.940.32041550.25443547X-RAY DIFFRACTION95.91
1.94-1.970.23571650.19263694X-RAY DIFFRACTION99.48
1.97-20.19591630.16973661X-RAY DIFFRACTION99.56
2-2.030.19961650.17123648X-RAY DIFFRACTION99.45
2.03-2.060.21261640.17283716X-RAY DIFFRACTION99.74
2.06-2.10.20221630.17413668X-RAY DIFFRACTION99.69
2.1-2.130.20351650.17493701X-RAY DIFFRACTION99.9
2.13-2.180.18871670.17493723X-RAY DIFFRACTION99.97
2.18-2.220.21921660.16483712X-RAY DIFFRACTION99.95
2.22-2.270.24391560.20273433X-RAY DIFFRACTION92.88
2.27-2.320.19031650.16533681X-RAY DIFFRACTION99.71
2.32-2.380.1911660.15893689X-RAY DIFFRACTION99.74
2.38-2.440.2021660.15663721X-RAY DIFFRACTION99.95
2.44-2.520.1891660.16073724X-RAY DIFFRACTION99.92
2.52-2.60.16411670.15753707X-RAY DIFFRACTION99.95
2.6-2.690.19011630.16363704X-RAY DIFFRACTION99.66
2.69-2.80.19121660.16863743X-RAY DIFFRACTION99.72
2.8-2.920.20071650.16653712X-RAY DIFFRACTION99.69
2.92-3.080.17991690.15853758X-RAY DIFFRACTION99.92
3.08-3.270.18971660.1583730X-RAY DIFFRACTION99.97
3.27-3.520.17221670.15673736X-RAY DIFFRACTION99.39
3.52-3.880.16881650.1373667X-RAY DIFFRACTION96.82
3.88-4.440.16571630.12493646X-RAY DIFFRACTION95.87
4.44-5.590.14231710.14533831X-RAY DIFFRACTION99.68
5.59-41.780.14471780.16543968X-RAY DIFFRACTION98.9
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)
11.125980829330.5600564313420.7727234928260.8483035804790.4416710721740.6413920214840.0563869197592-0.0113681933679-0.07894186272950.06793207910760.0341752255390.0391011436750.007674637570260.0003437906742260.0001103968120930.1263275578610.006102284965730.001067710022170.0944567044528-0.005425229574550.1780439260213.591941403914.227731733326.8815797234
20.6762076241970.483704251869-0.04622078752040.680733388060.273490592730.9157644054080.0183540082017-0.038017334752-0.07493329960020.08175139516320.0224829425658-0.02443244601210.1336133602790.002572355164540.000286995766490.128418182741-0.001338711884960.009889018918560.0992565480261-0.0001506781581770.096444148026827.920739714828.602407042946.5226778428
30.567925600562-0.09422634802560.07682529346931.2751115422-0.05395861848611.92456715122-0.045599578557-0.007977540798390.114219919670.04417876112970.00453076877978-0.112135500237-0.2710582437860.218017006259-0.02246269455390.108159447892-0.0482461589432-0.007748357473910.10969175890.01199843260080.086447679584631.588216724745.312962692926.3329473829
41.048744660390.735651679766-0.1547482976021.201623920940.4684246549111.60340681450.002429345219310.0877856873529-0.146073646593-0.05248057174260.0501446549417-0.09896734003710.1731882879250.1714940788030.01625974005970.1131205266850.000665400481864-0.006217572539710.133374562950.0005901857451690.095719506830433.4621797326.52504291112.6289058847
51.003633019261.30752049579-0.4935580737481.88434369261-0.1052696564632.29813881046-0.1319320479970.13220688366-0.546321175541-0.02515773160780.14579146181-0.6029635069250.1609095450210.753314520904-0.04125355239950.1035298187450.03083738502840.0001508727330770.251306043334-0.0464432449750.2214377442540.290749791327.07386590634.8270079811
60.8260389397040.4233232328190.526047231640.9819298049-0.4233832066471.21482015650.01364564437860.432107619319-0.826470198412-0.0392382081330.0887291968408-0.7722866220540.2769757474130.108489059588-0.2727064005770.1845311556830.0169961267014-0.003252348395170.138277803186-0.06597039304540.30942943452730.614184715311.534223451223.2348459056
71.37939415905-0.5595903603410.9958171298921.06842425756-0.6069875719250.7692202744880.1140402697760.102108146244-0.0483740446508-0.222007650279-0.0268998235085-0.06248528132780.06161744677810.06476298102470.001116871310630.1412487353760.01884822518130.02259622057380.1019839204810.005201200010750.16614524380382.999153276212.912618015216.6853099838
80.665089065526-0.46099074135-0.3453663420560.637330670626-0.07346883938540.875684797493-0.003340014850920.0869863176302-0.0366873727913-0.1014786454220.004603141910290.01830554881580.141476833289-0.0289691222986-2.80708353428E-50.1410020559160.004300341452720.002945155348750.1085260549740.004419415466110.095005240522969.087977411827.7011599633-3.17589056065
90.622482898166-0.08268117980610.09112242867161.176741776440.1192568015161.87825047062-0.007101396576090.005487561297890.0788992757032-0.0166074703735-0.01561939057090.0827017123276-0.289358398544-0.142492033196-0.009585335711790.1047218451890.0344720085096-0.002149440189110.0906290294339-0.002495570477330.093735142372765.729166853844.294398242817.0459579382
101.14229153602-0.809927095178-0.2138912079771.21386375739-0.5317324949471.64302556440.00351310695914-0.0831678211819-0.1565859794040.06759516099070.03849641497570.09203045039220.160464239425-0.1047071942640.01364126917390.1029062615560.006957507020420.001976861108010.1067464696660.0009801394114880.092475605374263.306087064525.838981594230.5768035771
111.14383234327-0.808329878067-0.8667301789131.935337280990.4031950599262.12949339464-0.2271638546120.120673704997-0.382032968803-0.0814560978330.01534062371110.514162922840.09166898292-0.540493166382-0.3889882071540.0931557629912-0.03073671794020.00068893615560.1904382142550.008713491693050.18774183466156.574345790126.48239368218.22624279558
120.881906020249-0.1760110830550.2160357919790.8996131549410.1932610392992.252098050910.149307939806-0.385387534809-0.735068485229-0.2610097939540.02102636728510.6938947638380.406316312347-0.109733819852-0.2333190038980.177483490069-0.00945585245308-0.04151684601190.08243717931620.06408906008740.28093330912965.743038267810.831723103319.832609011
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 - 259
44chain A and resid 496:575AA496 - 575260 - 339
55chain E or chain FF - EC - J1 - 4
66chain G or chain HG - HB - D1 - 4
77chain B and resid 236:329BE236 - 3291 - 94
88chain B and resid 330:386BE330 - 38695 - 151
99chain B and resid 387:495BE387 - 495152 - 260
1010chain B and resid 496:575BE496 - 575261 - 340
1111chain I or chain JJ - IG - I1 - 4
1212chain K or chain LK - LF - H1 - 4

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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