7M0A: DNA polymerase lambda

Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP. Determined by X-ray diffraction at 1.83 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 1.83 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 3,547
Mol. weight: 46.19 kDa
Ligands: CA, MG, PPV, TTP
Released: 16 Mar 2022

Explore 7M0A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M0A contains 25 α-helices and 10 β-strands across 1 chain. 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	240-242	3
α-helix	245-250	6
α-helix	254-269	16
α-helix	273-288	16
α-helix	296-301	6
α-helix	307-319	13
α-helix	323-326	4
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	385-386	2
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	427-433	7	2
α-helix	443-453	11
β-strand	457-462	6	2
β-strand	472-477	6	2
β-strand	487-493	7	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
α-helix	549	1
β-strand	550	1	3
α-helix	551-552	2
α-helix	556-562	7
α-helix	565-567	3
α-helix	570-573	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase lambda	A	protein	346	Homo sapiens	Q9UGP5 (AlphaFold model)
DNA (5'-d(cpgpgpcp*a)-3')	T	DNA	5	synthetic construct
DNA (5'-d(cpapgptpgpcp*t)-3')	P	DNA	7	synthetic construct
DNA (5'-d(pgpcpcpg)-3')	D	DNA	4	synthetic construct
DNA (5'-d(gpcpapcptpg)-3')	U	DNA	6	synthetic construct

Sequence of entity 1 (A), FASTA

>7M0A_1 DNA polymerase lambda (chains A)
GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSF
HKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTA
QMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSG
LLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQ
QQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSE
HALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW

Sequence of entity 2 (T), FASTA

>7M0A_2 DNA (5'-D(*CP*GP*GP*CP*A)-3') (chains T)
CGGCA

Sequence of entity 3 (P), FASTA

>7M0A_3 DNA (5'-D(*CP*AP*GP*TP*GP*CP*T)-3') (chains P)
CAGTGCT

Sequence of entity 4 (D), FASTA

>7M0A_4 DNA (5'-D(P*GP*CP*CP*G)-3') (chains D)
GCCG

Sequence of entity 5 (U), FASTA

>7M0A_5 DNA (5'-D(*GP*CP*AP*CP*TP*G)-3') (chains U)
GCACTG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
MG	Magnesium ion	Mg	2
PPV	Pyrophosphate	H4 O7 P2	1
TTP	Thymidine-5'-triphosphate	C10 H17 N2 O14 P3	1

Water and common crystallization additives (GOL, CL, NA) 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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