7M08: DNA polymerase lambda

Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP. Determined by X-ray diffraction at 1.7 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,365
Mol. weight: 45.5 kDa
Ligands: MG
Released: 16 Mar 2022

Explore 7M08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M08 contains 22 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: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	240-242	3
α-helix	245-248	4
α-helix	254-270	17
α-helix	273-288	16
α-helix	296-300	5
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	382-384	3
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	444-453	10
β-strand	457-463	7	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	549	1
β-strand	550	1	3
α-helix	551-552	2
α-helix	556-562	7
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(cpgpgpcpapgptpapcptp*g)-3')	T	DNA	11	synthetic construct
DNA (5'-d(cpapgptpapcp*t)-3')	P	DNA	7	synthetic construct
DNA (5'-d(pgpcpcpg)-3')	D	DNA	4	synthetic construct

Sequence of entity 1 (A), FASTA

>7M08_1 DNA polymerase lambda (chains A)
GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSF
HKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTA
QMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSG
LLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQ
QQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSE
HALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW

Sequence of entity 2 (T), FASTA

>7M08_2 DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3') (chains T)
CGGCAGTACTG

Sequence of entity 3 (P), FASTA

>7M08_3 DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3') (chains P)
CAGTACT

Sequence of entity 4 (D), FASTA

>7M08_4 DNA (5'-D(P*GP*CP*CP*G)-3') (chains D)
GCCG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (ACT, EDO, CL, NA) are not listed.

Primary citation

Comprehensive structural survey of DNA double-strand break synapsis by DNA Polymerase Lambda. Kaminski, A.M., Bebenek, K., Kunkel, T.A. et al. Not Published.

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
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
5III 1.8 Å, Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a…

Browse structure collections

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