4U7C: DNA polymerase kappa

Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA. Determined by X-ray diffraction at 2.8 Å resolution. Released 27 Jan 2016.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, unidentified
Chains: 6
Atoms: 7,889
Mol. weight: 127.74 kDa
Ligands: 0KX, MG
Released: 27 Jan 2016

Explore 4U7C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U7C contains 46 α-helices and 33 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: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	48-72	25
α-helix	76-95	20
β-strand	103-108	6	1
α-helix	111-118	8
α-helix	121-123	3
β-strand	128-131	4	2
β-strand	136-139	4	2
α-helix	141-144	4
α-helix	154-160	7
β-strand	165-167	3	2
α-helix	168-169	2
α-helix	171-185	15
β-strand	193-194	2	1
β-strand	199-203	5	1
α-helix	205-212	8
α-helix	216-218	3
β-strand	220-222	3	3
β-strand	283-285	3	3
α-helix	290-305	16
β-strand	309-314	6	1
α-helix	317-323	7
β-strand	332-334	3	1
α-helix	339-346	8
β-strand	350	1	4
α-helix	351-353	3
α-helix	359-367	9
β-strand	372	1	4
α-helix	373-378	6
α-helix	380-386	7
α-helix	389-400	12
β-strand	415-425	11	5
α-helix	428-449	22
β-strand	453-462	10	5
β-strand	467-478	12	5
α-helix	481-499	19
α-helix	503-504	2
β-strand	506-514	9	5

Chain B: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	6
α-helix	33-44	12
α-helix	48-72	25
α-helix	76-95	20
β-strand	103-108	6	7
α-helix	111-118	8
α-helix	121-123	3
β-strand	128-131	4	8
β-strand	136-139	4	8
α-helix	141-144	4
α-helix	154-160	7
β-strand	165-167	3	8
α-helix	168-169	2
α-helix	171-185	15
β-strand	193-194	2	7
β-strand	199-203	5	7
α-helix	205-211	7
α-helix	216-218	3
β-strand	220-222	3	9
β-strand	283-285	3	9
α-helix	290-305	16
β-strand	309-314	6	7
α-helix	317-323	7
β-strand	332-334	3	7
α-helix	339-346	8
β-strand	350	1	10
α-helix	351-353	3
α-helix	359-367	9
β-strand	372	1	10
α-helix	373-378	6
α-helix	380-386	7
α-helix	389-400	12
α-helix	407-409	3
α-helix	411-413	3
β-strand	415-425	11	11
α-helix	428-449	22
β-strand	453-462	10	11
β-strand	467-478	12	11
α-helix	481-499	19
α-helix	503-504	2
β-strand	506-514	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase kappa	A, B	protein	492	Homo sapiens	Q9UBT6 (AlphaFold model)
DNA (5'-d(pgpcpgpgpaptpcpap*g)-3')	C, P	DNA	9	unidentified
DNA (5'-d(paptpgp(vkj)pcptpgpaptpcpcpgpc)-3')	D, T	DNA	13	unidentified

Sequence of entity 1 (A, B), FASTA

>4U7C_1 DNA polymerase kappa (chains A, B)
GMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQV
DRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRF
GVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITK
HLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDP
FQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDK
NKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLL
FSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDL
QKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRL
RLMGVRISSFPN

Sequence of entity 2 (C, P), FASTA

>4U7C_2 DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3') (chains C, P)
GCGGATCAG

Sequence of entity 3 (D, T), FASTA

>4U7C_3 DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3') (chains D, T)
ATGXCTGATCCGC

Ligands and cofactors

ID	Name	Formula	Copies
0KX	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphory…	C9 H17 N4 O12 P3	2
MG	Magnesium ion	Mg	2

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

Primary citation

Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa. Jha, V., Bian, C., Xing, G. et al. Nucleic Acids Res (2016) 44:4957-4967. DOI 10.1093/nar/gkw204 · PubMed

Other PDB entries of the same protein (UniProt Q9UBT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CST 2.0 Å, Structure of human DNA polymerase kappa with DNA
1T94 2.4 Å, Crystal structure of the catalytic core of human DNA polymerase kappa
5W2C 2.5 Å, Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and…
4U6P 2.59 Å, Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human…
4BA9 2.73 Å, The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
6BRX 2.8 Å, Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major…
5W2A 2.9 Å, Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and…
5T14 3.0 Å, DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct
2OH2 3.05 Å, Ternary Complex of Human DNA Polymerase
6BS1 3.15 Å, Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major…
2W7O 3.16 Å, Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the…
3IN5 3.2 Å, Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion

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