7M4A: DNA polymerase lambda

DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 20 min. Determined by X-ray diffraction at 1.87 Å resolution. Released 6 Jul 2022.

Method: X-ray diffraction
Resolution: 1.87 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,079
Mol. weight: 44.02 kDa
Ligands: MN, PPV
Released: 6 Jul 2022

Explore 7M4A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M4A contains 20 α-helices and 12 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: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	254-269	16
α-helix	273-288	16
α-helix	292-293	2
α-helix	296-300	5
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	380-383	4
β-strand	387-388	2	1
α-helix	389-406	18
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	457-463	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
β-strand	537-538	2	4
β-strand	544-546	3	4
β-strand	549-550	2	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	329	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

>7M4A_1 DNA polymerase lambda (chains A)
AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACS
IPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLE
DIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRG
KATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRH
RRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVG
PGRVLPTPTEKDVFRLLGLPYREPAERDW

Sequence of entity 2 (T), FASTA

>7M4A_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

>7M4A_3 DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3') (chains P)
CAGTACT

Sequence of entity 4 (D), FASTA

>7M4A_4 DNA (5'-D(P*GP*CP*CP*G)-3') (chains D)
GCCG

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4
PPV	Pyrophosphate	H4 O7 P2	1

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

Primary citation

Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints. Jamsen, J.A., Shock, D.D., Wilson, S.H. Nat Commun (2022) 13:3193-3193. DOI 10.1038/s41467-022-30141-w · 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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