7M0D: DNA polymerase lambda

Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 10
Atoms: 7,458
Mol. weight: 92.56 kDa
Ligands: DUP, MG, CIT
Released: 16 Mar 2022

Explore 7M0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M0D contains 50 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	240-242	3
α-helix	245-248	4
α-helix	254-269	16
α-helix	273-288	16
α-helix	296-301	6
α-helix	307-319	13
α-helix	323-327	5
α-helix	332-339	8
α-helix	346-354	9
α-helix	360-366	7
α-helix	371-378	8
α-helix	380-384	5
α-helix	386	1
β-strand	387-388	2	1
α-helix	389-404	16
β-strand	411-414	4	2
α-helix	416-419	4
β-strand	424-425	2	1
β-strand	428-433	6	2
α-helix	443-453	11
β-strand	457-464	8	2
β-strand	471-478	8	2
α-helix	484-485	2
β-strand	486-493	8	2
α-helix	496-498	3
α-helix	499-507	9
α-helix	510-522	13
β-strand	525-527	3	3
β-strand	532-534	3	3
α-helix	535-536	2
β-strand	537-538	2	4
β-strand	544-546	3	4
α-helix	549	1
β-strand	550-551	2	3
α-helix	552	1
α-helix	556-562	7
α-helix	570-573	4

Chain B: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	240-242	3
α-helix	245-248	4
α-helix	254-269	16
α-helix	273-288	16
α-helix	296-301	6
α-helix	307-319	13
α-helix	323-327	5
α-helix	332-339	8
α-helix	346-354	9
α-helix	360-366	7
α-helix	371-378	8
α-helix	380-384	5
α-helix	386	1
β-strand	387-388	2	5
α-helix	389-404	16
β-strand	411-414	4	6
α-helix	416-419	4
β-strand	424-425	2	5
β-strand	428-433	6	6
α-helix	443-453	11
β-strand	457-467	11	6
β-strand	470-478	9	6
α-helix	484-485	2
β-strand	486-493	8	6
α-helix	496-498	3
α-helix	499-507	9
α-helix	510-522	13
β-strand	525-527	3	7
β-strand	532-534	3	7
α-helix	535-536	2
β-strand	537-538	2	8
β-strand	544-546	3	8
α-helix	549	1
β-strand	550-551	2	7
α-helix	552	1
α-helix	556-562	7
α-helix	570-572	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase lambda	A, B	protein	346	Homo sapiens	Q9UGP5 (AlphaFold model)
DNA (5'-d(cpgpgpcpapgp*c)-3')	G, K	DNA	7	synthetic construct
DNA (5'-d(cpapgptpgpc)-3')	F, J	DNA	6	synthetic construct
DNA (5'-d(pgpcpcpg)-3')	H, L	DNA	4	synthetic construct
DNA (5'-d(apcptpg)-3')	E, I	DNA	4	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7M0D_1 DNA polymerase lambda (chains A, B)
GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSF
HKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTA
QMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSG
LLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQ
QQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSE
HALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW

Sequence of entity 2 (G, K), FASTA

>7M0D_2 DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') (chains G, K)
CGGCAGC

Sequence of entity 3 (F, J), FASTA

>7M0D_3 DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') (chains F, J)
CAGTGC

Sequence of entity 4 (H, L), FASTA

>7M0D_4 DNA (5'-D(P*GP*CP*CP*G)-3') (chains H, L)
GCCG

Sequence of entity 5 (E, I), FASTA

>7M0D_5 DNA (5'-D(*AP*CP*TP*G)-3') (chains E, I)
ACTG

Ligands and cofactors

ID	Name	Formula	Copies
DUP	2'-deoxyuridine 5'-alpha,beta-imido-triphosphate	C9 H16 N3 O13 P3	2
MG	Magnesium ion	Mg	2
CIT	Citric acid	C6 H8 O7	2

Water and common crystallization additives (K, NA, FMT, CL, EDO, TRS) are not listed.

Primary citation

Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining. Kaminski, A.M., Chiruvella, K.K., Ramsden, D.A. et al. Nat Commun (2022) 13:3806-3806. DOI 10.1038/s41467-022-31278-4 · PubMed

Other PDB entries of the same protein (UniProt Q9UGP5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M07 1.57 Å, Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M49 1.6 Å, DNA Polymerase Lambda, TTP:At Mn2+ Reaction State Ternary Complex, 5 min
9NPU 1.63 Å, Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M47 1.65 Å, DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 60 min
2BCQ 1.65 Å, DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp
7M09 1.65 Å, Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate…
7M4B 1.66 Å, DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min
7M08 1.7 Å, Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M4L 1.7 Å, DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min
7M4K 1.72 Å, DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex
5IIJ 1.72 Å, Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a…
2BCR 1.75 Å, DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp

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