7NV1: Human Pol Kappa holoenzyme with Ub-PCNA

Human Pol Kappa holoenzyme with Ub-PCNA. Determined by electron microscopy at 6.4 Å resolution. Released 3 Nov 2021.

Method: Electron microscopy
Resolution: 6.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 9,928
Mol. weight: 206.04 kDa
Ligands: TTP
Released: 3 Nov 2021

Explore 7NV1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NV1 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	9
α-helix	111-117	7
β-strand	128-130	3	10
β-strand	139	1	10
α-helix	141-144	4
β-strand	165-167	3	10
α-helix	174-188	15
β-strand	193	1	9
β-strand	201-203	3	9
α-helix	209-211	3
α-helix	284-286	3
α-helix	290-305	16
β-strand	312-314	3	9
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	11
α-helix	429-447	19
β-strand	453-462	10	11
β-strand	467-478	12	11
α-helix	485-496	12
β-strand	506-514	9	11

Chain B: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-19	10
β-strand	25-31	7	2
β-strand	34-40	7	2
β-strand	47-52	6	2
β-strand	59-61	3	1
β-strand	66-71	6	2
α-helix	72-78	7
β-strand	87-92	6	1
β-strand	98-104	7	1
β-strand	110-117	8	1
β-strand	119	1	2
β-strand	135-140	6	2
α-helix	141-152	12
β-strand	157-162	6	3
β-strand	166-170	5	3
β-strand	181-183	3	3
β-strand	196-199	4	2
β-strand	203-208	6	3
α-helix	209-215	7
α-helix	216-218	3
β-strand	224-229	6	2
α-helix	234	1
β-strand	235-239	5	2
β-strand	245-251	7	2

Chain C: 5 helices, 19 β-strands

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

Chain D: 6 helices, 19 β-strands

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

Molecules and chains

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

Sequence of entity 1 (B, C, D), FASTA

>7NV1_1 Proliferating cell nuclear antigen (chains B, C, D)
GPHMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGF
DTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMK
LMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGN
GNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVV
EYKIADMGHLKYYLAPKIEDEEGS

Sequence of entity 2 (A), FASTA

>7NV1_2 DNA polymerase kappa (chains A)
MDSTKEKCDSYKDDLLLRMGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQV
NQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDN
PELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKE
VKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNK
LSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFR
IEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKV
TEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVER
TFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVST
AEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKHQQRSIIGFLQAGNQAL
SATECTLEKTDKDKFVKPLEMSHKKSFFDKKRSERKWSHQDTFKCEAVNKQSFQTSQPFQ
VLKKKMNENLEISENSDDCQILTCPVCFRAQGCISLEALNKHVDECLDGPSISENFKMFS
CSHVSATKVNKKENVPASSLCEKQDYEAHPKIKEISSVDCIALVDTIDNSSKAESIDALS
NKHSKEECSSLPSKSFNIEHCHQNSSSTVSLENEDVGSFRQEYRQPYLCEVKTGQALVCP
VCNVEQKTSDLTLFNVHVDVCLNKSFIQELRKDKFNPVNQPKESSRSTGSSSGVQKAVTR
TKRPGLMTKYSTSKKIKPNNPKHTLDIFFK

Sequence of entity 3 (P), FASTA

>7NV1_3 DNA Primer (chains P)
AGCTATGACCATGATTACGAATTGC

Sequence of entity 4 (T), FASTA

>7NV1_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 P12004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U7B 1.88 Å, Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1)
8F5Q 1.9 Å, Crystal structure of human PCNA in complex with the PIP box of FBH1
9N3L 1.9 Å, Co-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112
5E0U 1.93 Å, Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms
5MLO 1.96 Å, Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide
4RJF 2.01 Å, Crystal structure of the human sliding clamp at 2.0 angstrom resolution
5E0V 2.07 Å, Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms
3VKX 2.1 Å, Structure of PCNA
6HVO 2.1 Å, Crystal structure of human PCNA in complex with three peptides of p12 subunit of human…
4ZTD 2.2 Å, Crystal Structure of Human PCNA in complex with a TRAIP peptide
5YCO 2.2 Å, Complex structure of PCNA with UHRF2
5MOM 2.27 Å, Crystal Structure of PCNA encoding the hypomorphic mutation S228I

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