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

ID or keywords:

Entry

Database: PDB / ID: 7m0d

Title

Pre-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

Keywords

TRANSFERASE / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Kaminski, A.M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A.

Funding support

United States, 2items

Organization	Grant number	Country
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

Citation

Journal: 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

Deposition	Mar 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2023	Group: 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 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7m0d.cif.gz	400.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7m0d.ent.gz	281.3 KB	Display	PDB format
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Validation report

Summary document	7m0d_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7m0d_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7m0d_validation.xml.gz	40.9 KB	Display
Data in CIF	7m0d_validation.cif.gz	63.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m0/7m0d ftp://data.pdbj.org/pub/pdb/validation_reports/m0/7m0d	HTTPS FTP

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Related structure data

Related structure data	7m07C 7m09C 7m0aC 7m0bC 7m0eC 2pfoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4k4g-2 3mgh-1 1xsl-3 4k4g-3 4k4i-2 2gws-3 1bgv-d 1rzt-1 5iio-4 3c5f-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#3 - Mar 2000 DNA Polymerase similarity (16) #55 - Jul 2004 DNA Ligase similarity (4) #150 - Jun 2012 Sliding Clamps similarity (3) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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

92.6 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author
Evidence: gel filtration
46.3 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author
46.3 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
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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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

#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(CPGPGPCPAPGPC)-3') Mass: 2123.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#3: DNA chain	DNA (5'-D(CPAPGPTPGPC)-3') Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	DNA (5'-D(PGPCPCPG)-3') Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain	DNA (5'-D(APCPTPG)-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 interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.03 Å³/Da / Density % sol: 69.5 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2020
Radiation	Monochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 115616 / % possible obs: 99.1 % / Redundancy: 6.5 % / B_iso Wilson estimate: 18.04 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_sym value: 0.102 / Χ²: 0.578 / Net I/σ(I): 17.4
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 5755 / CC_1/2: 0.859 / CC star: 0.961 / R_sym value: 0.927 / Χ²: 0.364 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1887	4939	4.28 %	random
R_work	0.1643	110517	-	-
obs	0.1654	115456	98.82 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 22.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→41.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5280	846	166	1076	7368

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0093	6558
X-RAY DIFFRACTION	f_angle_d	1.0333	9039
X-RAY DIFFRACTION	f_chiral_restr	0.0568	983
X-RAY DIFFRACTION	f_plane_restr	0.0074	1019
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9243	1012

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.82	0.3013	152	0.2391	3393	X-RAY DIFFRACTION	92.97
1.82-1.84	0.2299	166	0.2187	3703	X-RAY DIFFRACTION	99.9
1.84-1.86	0.2426	164	0.2127	3674	X-RAY DIFFRACTION	99.95
1.86-1.89	0.2546	164	0.2076	3671	X-RAY DIFFRACTION	99.87
1.89-1.91	0.2498	161	0.2292	3556	X-RAY DIFFRACTION	96.62
1.91-1.94	0.3204	155	0.2544	3547	X-RAY DIFFRACTION	95.91
1.94-1.97	0.2357	165	0.1926	3694	X-RAY DIFFRACTION	99.48
1.97-2	0.1959	163	0.1697	3661	X-RAY DIFFRACTION	99.56
2-2.03	0.1996	165	0.1712	3648	X-RAY DIFFRACTION	99.45
2.03-2.06	0.2126	164	0.1728	3716	X-RAY DIFFRACTION	99.74
2.06-2.1	0.2022	163	0.1741	3668	X-RAY DIFFRACTION	99.69
2.1-2.13	0.2035	165	0.1749	3701	X-RAY DIFFRACTION	99.9
2.13-2.18	0.1887	167	0.1749	3723	X-RAY DIFFRACTION	99.97
2.18-2.22	0.2192	166	0.1648	3712	X-RAY DIFFRACTION	99.95
2.22-2.27	0.2439	156	0.2027	3433	X-RAY DIFFRACTION	92.88
2.27-2.32	0.1903	165	0.1653	3681	X-RAY DIFFRACTION	99.71
2.32-2.38	0.191	166	0.1589	3689	X-RAY DIFFRACTION	99.74
2.38-2.44	0.202	166	0.1566	3721	X-RAY DIFFRACTION	99.95
2.44-2.52	0.189	166	0.1607	3724	X-RAY DIFFRACTION	99.92
2.52-2.6	0.1641	167	0.1575	3707	X-RAY DIFFRACTION	99.95
2.6-2.69	0.1901	163	0.1636	3704	X-RAY DIFFRACTION	99.66
2.69-2.8	0.1912	166	0.1686	3743	X-RAY DIFFRACTION	99.72
2.8-2.92	0.2007	165	0.1665	3712	X-RAY DIFFRACTION	99.69
2.92-3.08	0.1799	169	0.1585	3758	X-RAY DIFFRACTION	99.92
3.08-3.27	0.1897	166	0.158	3730	X-RAY DIFFRACTION	99.97
3.27-3.52	0.1722	167	0.1567	3736	X-RAY DIFFRACTION	99.39
3.52-3.88	0.1688	165	0.137	3667	X-RAY DIFFRACTION	96.82
3.88-4.44	0.1657	163	0.1249	3646	X-RAY DIFFRACTION	95.87
4.44-5.59	0.1423	171	0.1453	3831	X-RAY DIFFRACTION	99.68
5.59-41.78	0.1447	178	0.1654	3968	X-RAY DIFFRACTION	98.9

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.12598082933	0.560056431342	0.772723492826	0.848303580479	0.441671072174	0.641392021484	0.0563869197592	-0.0113681933679	-0.0789418627295	0.0679320791076	0.034175225539	0.039101143675	0.00767463757026	0.000343790674226	0.000110396812093	0.126327557861	0.00610228496573	0.00106771002217	0.0944567044528	-0.00542522957455	0.17804392602	13.5919414039	14.2277317333	26.8815797234
2	0.676207624197	0.483704251869	-0.0462207875204	0.68073338806	0.27349059273	0.915764405408	0.0183540082017	-0.038017334752	-0.0749332996002	0.0817513951632	0.0224829425658	-0.0244324460121	0.133613360279	0.00257235516454	0.00028699576649	0.128418182741	-0.00133871188496	0.00988901891856	0.0992565480261	-0.000150678158177	0.0964441480268	27.9207397148	28.6024070429	46.5226778428
3	0.567925600562	-0.0942263480256	0.0768252934693	1.2751115422	-0.0539586184861	1.92456715122	-0.045599578557	-0.00797754079839	0.11421991967	0.0441787611297	0.00453076877978	-0.112135500237	-0.271058243786	0.218017006259	-0.0224626945539	0.108159447892	-0.0482461589432	-0.00774835747391	0.1096917589	0.0119984326008	0.0864476795846	31.5882167247	45.3129626929	26.3329473829
4	1.04874466039	0.735651679766	-0.154748297602	1.20162392094	0.468424654911	1.6034068145	0.00242934521931	0.0877856873529	-0.146073646593	-0.0524805717426	0.0501446549417	-0.0989673400371	0.173188287925	0.171494078803	0.0162597400597	0.113120526685	0.000665400481864	-0.00621757253971	0.13337456295	0.000590185745169	0.0957195068304	33.46217973	26.525042911	12.6289058847
5	1.00363301926	1.30752049579	-0.493558073748	1.88434369261	-0.105269656463	2.29813881046	-0.131932047997	0.13220688366	-0.546321175541	-0.0251577316078	0.14579146181	-0.602963506925	0.160909545021	0.753314520904	-0.0412535523995	0.103529818745	0.0308373850284	0.000150872733077	0.251306043334	-0.046443244975	0.22143774425	40.2907497913	27.073865906	34.8270079811
6	0.826038939704	0.423323232819	0.52604723164	0.9819298049	-0.423383206647	1.2148201565	0.0136456443786	0.432107619319	-0.826470198412	-0.039238208133	0.0887291968408	-0.772286622054	0.276975747413	0.108489059588	-0.272706400577	0.184531155683	0.0169961267014	-0.00325234839517	0.138277803186	-0.0659703930454	0.309429434527	30.6141847153	11.5342234512	23.2348459056
7	1.37939415905	-0.559590360341	0.995817129892	1.06842425756	-0.606987571925	0.769220274488	0.114040269776	0.102108146244	-0.0483740446508	-0.222007650279	-0.0268998235085	-0.0624852813278	0.0616174467781	0.0647629810247	0.00111687131063	0.141248735376	0.0188482251813	0.0225962205738	0.101983920481	0.00520120001075	0.166145243803	82.9991532762	12.9126180152	16.6853099838
8	0.665089065526	-0.46099074135	-0.345366342056	0.637330670626	-0.0734688393854	0.875684797493	-0.00334001485092	0.0869863176302	-0.0366873727913	-0.101478645422	0.00460314191029	0.0183055488158	0.141476833289	-0.0289691222986	-2.80708353428E-5	0.141002055916	0.00430034145272	0.00294515534875	0.108526054974	0.00441941546611	0.0950052405229	69.0879774118	27.7011599633	-3.17589056065
9	0.622482898166	-0.0826811798061	0.0911224286716	1.17674177644	0.119256801516	1.87825047062	-0.00710139657609	0.00548756129789	0.0788992757032	-0.0166074703735	-0.0156193905709	0.0827017123276	-0.289358398544	-0.142492033196	-0.00958533571179	0.104721845189	0.0344720085096	-0.00214944018911	0.0906290294339	-0.00249557047733	0.0937351423727	65.7291668538	44.2943982428	17.0459579382
10	1.14229153602	-0.809927095178	-0.213891207977	1.21386375739	-0.531732494947	1.6430255644	0.00351310695914	-0.0831678211819	-0.156585979404	0.0675951609907	0.0384964149757	0.0920304503922	0.160464239425	-0.104707194264	0.0136412691739	0.102906261556	0.00695750702042	0.00197686110801	0.106746469666	0.000980139411488	0.0924756053742	63.3060870645	25.8389815942	30.5768035771
11	1.14383234327	-0.808329878067	-0.866730178913	1.93533728099	0.403195059926	2.12949339464	-0.227163854612	0.120673704997	-0.382032968803	-0.081456097833	0.0153406237111	0.51416292284	0.09166898292	-0.540493166382	-0.388988207154	0.0931557629912	-0.0307367179402	0.0006889361556	0.190438214255	0.00871349169305	0.187741834661	56.5743457901	26.4823936821	8.22624279558
12	0.881906020249	-0.176011083055	0.216035791979	0.899613154941	0.193261039299	2.25209805091	0.149307939806	-0.385387534809	-0.735068485229	-0.261009793954	0.0210263672851	0.693894763838	0.406316312347	-0.109733819852	-0.233319003898	0.177483490069	-0.00945585245308	-0.0415168460119	0.0824371793162	0.0640890600874	0.280933309129	65.7430382678	10.8317231033	19.832609011

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain A and resid 237:329	A	A	237 - 329	1 - 93
2	2	chain A and resid 330:386	A	A	330 - 386	94 - 150
3	3	chain A and resid 387:495	A	A	387 - 495	151 - 259
4	4	chain A and resid 496:575	A	A	496 - 575	260 - 339
5	5	chain E or chain F	F - E	C - J	1 - 4
6	6	chain G or chain H	G - H	B - D	1 - 4
7	7	chain B and resid 236:329	B	E	236 - 329	1 - 94
8	8	chain B and resid 330:386	B	E	330 - 386	95 - 151
9	9	chain B and resid 387:495	B	E	387 - 495	152 - 260
10	10	chain B and resid 496:575	B	E	496 - 575	261 - 340
11	11	chain I or chain J	J - I	G - I	1 - 4
12	12	chain K or chain L	K - L	F - H	1 - 4

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Protein , 1 types, 2 molecules AB

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DNA chain , 4 types, 8 molecules GKFJHLIE

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Non-polymers , 10 types, 1108 molecules

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