7NV0: Human Pol Kappa holoenzyme with wt PCNA

Human Pol Kappa holoenzyme with wt PCNA. Determined by electron microscopy at 3.4 Å resolution. Released 10 Nov 2021.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 9,928
Mol. weight: 206.04 kDa
Ligands: TTP
Released: 10 Nov 2021

Explore 7NV0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NV0 contains 33 α-helices and 68 β-strands across 4 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: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	48-71	24
α-helix	81-94	14
β-strand	103-105	3	1
α-helix	111-117	7
β-strand	128-130	3	2
β-strand	139	1	2
α-helix	141-144	4
β-strand	165-167	3	2
α-helix	174-188	15
β-strand	193	1	1
β-strand	201-203	3	1
α-helix	209-211	3
α-helix	284-286	3
α-helix	290-305	16
β-strand	312-314	3	1
α-helix	317-323	7
α-helix	343-346	4
α-helix	360-366	7
α-helix	373-377	5
α-helix	380-386	7
α-helix	389-399	11
β-strand	415-421	7	3
α-helix	429-447	19
β-strand	453-462	10	3
β-strand	467-478	12	3
α-helix	485-496	12
β-strand	506-514	9	3

Chain B: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	10-19	10
β-strand	25-31	7	5
β-strand	34-40	7	5
β-strand	47-52	6	5
β-strand	59-61	3	4
β-strand	66-71	6	5
α-helix	72-78	7
β-strand	87-92	6	4
β-strand	98-104	7	4
β-strand	110-117	8	4
β-strand	119	1	5
β-strand	135-140	6	5
α-helix	141-151	11
β-strand	157-162	6	6
β-strand	166-170	5	6
β-strand	181-183	3	6
β-strand	196-199	4	5
β-strand	203-208	6	6
α-helix	209-215	7
α-helix	216-218	3
β-strand	224-229	6	5
α-helix	234	1
β-strand	235-239	5	5
β-strand	245-251	7	5

Chain C: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
α-helix	12-15	4
β-strand	26-30	5	8
β-strand	34-40	7	9
β-strand	47-53	7	9
β-strand	59-61	3	7
β-strand	66-70	5	8
α-helix	72-79	8
β-strand	87-92	6	7
β-strand	98-104	7	7
β-strand	110-117	8	7
β-strand	119	1	8
β-strand	135-140	6	9
α-helix	141-154	14
β-strand	157-163	7	4
β-strand	166-171	6	4
β-strand	178-182	5	4
β-strand	196-199	4	9
β-strand	203-208	6	4
α-helix	215-217	3
α-helix	219-221	3
β-strand	224-230	7	9
β-strand	233-240	8	9
β-strand	245-251	7	9

Chain D: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	10
α-helix	10-18	9
β-strand	25-31	7	11
β-strand	34-40	7	11
β-strand	46-53	8	11
β-strand	59-61	3	10
β-strand	66-71	6	11
α-helix	72-78	7
β-strand	88-92	5	10
β-strand	98-102	5	10
β-strand	114-117	4	10
β-strand	119	1	11
α-helix	128-130	3
β-strand	135-140	6	11
α-helix	141-148	8
β-strand	158-162	5	7
β-strand	166-173	8	7
β-strand	176-183	8	7
β-strand	196-197	2	11
β-strand	204-207	4	7
α-helix	209-215	7
α-helix	219-221	3
β-strand	224-229	6	11
β-strand	235-241	7	11
β-strand	245-251	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase kappa	A	protein	870	Homo sapiens	Q9UBT6 (AlphaFold model)
Proliferating cell nuclear antigen	B, C, D	protein	264	Homo sapiens	P12004 (AlphaFold model)
DNA Primer	P	DNA	25	synthetic construct
DNA Template	T	DNA	38	synthetic construct

Sequence of entity 1 (A), FASTA

>7NV0_1 DNA polymerase kappa (chains A)
MDSTKEKCDSYKDDLLLRMGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQV
NQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDN
PELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKE
VKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNK
LSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFR
IEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKV
TEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVER
TFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVST
AEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKHQQRSIIGFLQAGNQAL
SATECTLEKTDKDKFVKPLEMSHKKSFFDKKRSERKWSHQDTFKCEAVNKQSFQTSQPFQ
VLKKKMNENLEISENSDDCQILTCPVCFRAQGCISLEALNKHVDECLDGPSISENFKMFS
CSHVSATKVNKKENVPASSLCEKQDYEAHPKIKEISSVDCIALVDTIDNSSKAESIDALS
NKHSKEECSSLPSKSFNIEHCHQNSSSTVSLENEDVGSFRQEYRQPYLCEVKTGQALVCP
VCNVEQKTSDLTLFNVHVDVCLNKSFIQELRKDKFNPVNQPKESSRSTGSSSGVQKAVTR
TKRPGLMTKYSTSKKIKPNNPKHTLDIFFK

Sequence of entity 2 (B, C, D), FASTA

>7NV0_2 Proliferating cell nuclear antigen (chains B, C, D)
GPHMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGF
DTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMK
LMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGN
GNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVV
EYKIADMGHLKYYLAPKIEDEEGS

Sequence of entity 3 (P), FASTA

>7NV0_3 DNA Primer (chains P)
AGCTATGACCATGATTACGAATTGC

Sequence of entity 4 (T), FASTA

>7NV0_4 DNA Template (chains T)
CTGCACGAATTAAGCAATTCGTAATCATGGTCATAGCT

Ligands and cofactors

ID	Name	Formula	Copies
TTP	Thymidine-5'-triphosphate	C10 H17 N2 O14 P3	1

Primary citation

Cryo-EM structure of human Pol kappa bound to DNA and mono-ubiquitylated PCNA. Lancey, C., Tehseen, M., Bakshi, S. et al. Nat Commun (2021) 12:6095-6095. DOI 10.1038/s41467-021-26251-6 · 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
4U7C 2.8 Å, Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA
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…

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