6S1N: Human polymerase delta holoenzyme Conformer 2

Human polymerase delta holoenzyme Conformer 2. Determined by electron microscopy at 4.86 Å resolution. Released 25 Dec 2019.

Method: Electron microscopy
Resolution: 4.86 Å
Organisms: Homo sapiens, synthetic construct
Chains: 9
Atoms: 19,726
Mol. weight: 351.43 kDa
Ligands: ZN, SF4, TTP
Released: 25 Dec 2019

Explore 6S1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S1N contains 82 α-helices and 127 β-strands across 7 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: 41 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	79-83	5
β-strand	94-105	12	1
β-strand	123-131	9	1
β-strand	136-142	7	1
β-strand	147-151	5	2
α-helix	152-153	2
α-helix	161-168	8
α-helix	170-171	2
α-helix	174-176	3
β-strand	192-195	4	2
β-strand	197	1	3
β-strand	207-213	7	2
α-helix	217-219	3
α-helix	220-227	8
β-strand	245	1	2
α-helix	250-258	9
β-strand	265-268	4	1
β-strand	282	1	4
β-strand	286-291	6	1
β-strand	296-298	3	1
α-helix	299	1
α-helix	302-305	4
β-strand	311-319	9	5
α-helix	325-327	3
β-strand	334-343	10	5
β-strand	351-356	6	5
β-strand	367-370	4	5
α-helix	374-388	15
β-strand	392-395	4	5
α-helix	398-402	5
α-helix	403-412	10
β-strand	424	1	4
β-strand	431-438	8	6
β-strand	442-449	8	6
β-strand	455-458	4	5
α-helix	459-466	8
α-helix	474-481	8
α-helix	494-498	5
α-helix	502-525	24
α-helix	528-539	12
α-helix	545-547	3
α-helix	552-563	12
β-strand	569	1	3
β-strand	586	1	7
α-helix	587-589	3
β-strand	592-594	3	8
β-strand	598-603	6	8
α-helix	606-613	8
α-helix	618-620	3
β-strand	621-622	2	9
α-helix	623	1
β-strand	637-639	3	9
β-strand	645-647	3	9
α-helix	656-674	19
α-helix	680-704	25
α-helix	714-738	25
β-strand	750-754	5	8
β-strand	755	1	7
β-strand	758-762	5	8
α-helix	768-782	15
β-strand	792-805	14	8
β-strand	808-814	7	8
β-strand	824-827	4	8
α-helix	838-852	15
α-helix	857-872	16
β-strand	883-886	4	10
α-helix	899-905	7
β-strand	921-924	4	10
β-strand	925-926	2	11
β-strand	927	1	12
β-strand	939-940	2	11
α-helix	942-948	7
β-strand	952	1	12
α-helix	954-956	3
α-helix	957-962	6
α-helix	963-970	8
α-helix	977-987	11
α-helix	1002-1004	3
β-strand	1011	1	13
β-strand	1018	1	13
α-helix	1034-1055	22
α-helix	1057-1062	6
α-helix	1078-1095	18

Chain B: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	24	1	14
α-helix	26-28	3
α-helix	37-39	3
α-helix	51-73	23
β-strand	79	1	15
α-helix	85-86	2
β-strand	87	1	15
β-strand	91-100	10	15
β-strand	132-136	5	15
β-strand	141-143	3	15
β-strand	145-146	2	15
β-strand	158-165	8	15
β-strand	171-177	7	15
α-helix	181-183	3
α-helix	185-189	5
β-strand	195-199	5	16
α-helix	210-223	14
α-helix	229-235	7
β-strand	238-244	7	16
α-helix	273-287	15
β-strand	292-295	4	16
α-helix	308-312	5
α-helix	313-315	3
α-helix	319-321	3
β-strand	322	1	17
β-strand	325-327	3	16
β-strand	332-336	5	18
β-strand	339-343	5	18
α-helix	348-354	7
α-helix	361-370	10
β-strand	373	1	19
β-strand	394	1	19
β-strand	401-403	3	18
β-strand	411-416	6	18
β-strand	422-427	6	18
β-strand	436-441	6	16
β-strand	447-454	8	16

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	21-22	2	16
α-helix	25-29	5
α-helix	34-51	18
β-strand	58-68	11	16
β-strand	73-80	8	16
α-helix	85-91	7
β-strand	97-104	8	16
α-helix	113-123	11
β-strand	135	1	14
β-strand	142	1	17

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	45-52	8
α-helix	66-76	11

Chain E: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	20
α-helix	10-17	8
β-strand	25-31	7	21
β-strand	34-40	7	21
β-strand	46-53	8	21
α-helix	54-56	3
β-strand	60-61	2	20
β-strand	66-71	6	21
α-helix	72-79	8
β-strand	87-92	6	20
β-strand	98-104	7	20
β-strand	112-117	6	20
α-helix	127-129	3
β-strand	135-140	6	21
α-helix	141-152	12
β-strand	157-162	6	22
β-strand	166-171	6	22
β-strand	178-183	6	22
β-strand	196-199	4	21
β-strand	203-208	6	22
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	21
β-strand	235-241	7	21
β-strand	245-251	7	21

Chain F: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	23
α-helix	9-19	11
β-strand	25-28	4	24
β-strand	29-30	2	25
β-strand	34-40	7	25
β-strand	47-53	7	25
β-strand	59-62	4	23
β-strand	68-71	4	24
α-helix	72-78	7
β-strand	87-92	6	23
β-strand	98-104	7	23
β-strand	110-117	8	23
β-strand	135-140	6	25
α-helix	141-151	11
β-strand	157-162	6	20
β-strand	166-171	6	20
β-strand	177-183	7	20
β-strand	196-199	4	25
β-strand	203-208	6	20
α-helix	209-215	7
α-helix	219-221	3
β-strand	224-229	6	25
β-strand	235-241	7	25
β-strand	245-251	7	25
α-helix	252-254	3

Chain G: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	26
α-helix	9-19	11
β-strand	25-30	6	27
β-strand	34-40	7	27
β-strand	47-53	7	27
β-strand	59-62	4	26
β-strand	66-71	6	27
α-helix	72-78	7
β-strand	87-92	6	26
β-strand	98-104	7	26
β-strand	111-117	7	26
β-strand	135-140	6	27
α-helix	141-154	14
β-strand	157-162	6	23
β-strand	166-173	8	23
β-strand	176-183	8	23
β-strand	196-199	4	27
β-strand	204-208	5	23
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	27
β-strand	235-241	7	27
β-strand	245-251	7	27
α-helix	252-253	2
β-strand	254	1	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase delta catalytic subunit	A	protein	1107	Homo sapiens	P28340 (AlphaFold model)
DNA polymerase delta subunit 2	B	protein	469	Homo sapiens	P49005 (AlphaFold model)
DNA polymerase delta subunit 3	C	protein	474	Homo sapiens	Q15054 (AlphaFold model)
DNA polymerase delta subunit 4	D	protein	137	Homo sapiens	Q9HCU8 (AlphaFold model)
Proliferating cell nuclear antigen	E, F, G	protein	264	Homo sapiens	P12004
DNA primer	P	DNA	25	synthetic construct
DNA template	T	DNA	38	synthetic construct

Sequence of entity 1 (A), FASTA

>6S1N_1 DNA polymerase delta catalytic subunit (chains A)
MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQS
VLEGVADGQVPPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRG
SVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRDSRGGR
ELTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRVAGLGTPS
FAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEKATQCQLEADVLWSDVVSHPP
EGPWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPC
APILGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF
LGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFH
FLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTG
VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIAT
LDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQIL
ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSV
TGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAAD
WVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV
ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQAH
VELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQ
QLAKPLLRIFEPILGEGRAEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLS
HQGAVCEFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFY
MRKKVRKDLEDQEQLLRRFGPPGPEAW

Sequence of entity 2 (B), FASTA

>6S1N_2 DNA polymerase delta subunit 2 (chains B)
MFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHIYATRLIQ
MRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQ
PPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFAD
LAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSR
VILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFD
PTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMED
HLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPED
QTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP

Sequence of entity 3 (C), FASTA

>6S1N_3 DNA polymerase delta subunit 3 (chains C)
MWSHPQFEKADQLYLENIDEFVTDQNKIVTYKWLSYTLGVHVNQAKQMLYDYVERKRKEN
SGAQLHVTYLVSGSLIQNGHSCHKVAVVREDKLEAVKSKLAVTASIHVYSIQKAMLKDSG
PLFNTDYDILKSNLQNCSKFSAIQCAAAVPRAPAESSSSSKKFEQSHLHMSSETQANNEL
TTNGHGPPASKQVSQQPKGIMGMFASKAAAKTQETNKETKTEAKEVTNASAAGNKAPGKG
NMMSNFFGKAAMNKFKVNLDSEQAVKEEKIVEQPTVSVTEPKLATPAGLKKSSKKAEPVK
VLQKEKKRGKRVALSDDETKETENMRKKRRRIKLPESDSSEDEVFPDSPGAYEAESPSPP
PPPSPPLEPVPKTEPEPPSVKSSSGENKRKRKRVLKSKTYLDGEGCIVTEKVYESESCTD
SEEELNMKTSSVHRPPAMTVKKEPREERKGPKKGTAALGKANRQVSITGFFQRK

Sequence of entity 4 (D), FASTA

>6S1N_4 DNA polymerase delta subunit 4 (chains D)
MHHHHHHSRAWRHPQFGGHHHHHHENLYFQSGRKRLITDSYPVVKRREGPAGHSKGELAP
ELGEEPQPRDEEEAELELLRQFDLAWQYGPCTGITRLQRWCRAKQMGLEPPPEVWQVLKT
HPGDPRFQCSLWHLYPL

Sequence of entity 5 (E, F, G), FASTA

>6S1N_5 Proliferating cell nuclear antigen (chains E, F, G)
GPHMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGF
DTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMK
LMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGN
GNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVV
EYKIADMGHLKYYLAPKIEDEEGS

Sequence of entity 6 (P), FASTA

>6S1N_6 DNA primer (chains P)
AGCTATGACCATGATTACGAATTGC

Sequence of entity 7 (T), FASTA

>6S1N_7 DNA template (chains T)
CTGCACGAATTAAGCAATTCGTAATCATGGTCATAGCT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
SF4	Iron/sulfur cluster	Fe4 S4	1
TTP	Thymidine-5'-triphosphate	C10 H17 N2 O14 P3	1

Primary citation

Structure of the processive human Pol delta holoenzyme. Lancey, C., Tehseen, M., Raducanu, V.S. et al. Nat Commun (2020) 11:1109-1109. DOI 10.1038/s41467-020-14898-6 · PubMed

Other PDB entries of the same protein (UniProt P28340 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TNY 3.08 Å, Processive human polymerase delta holoenzyme
9EKB 3.65 Å, Cryo-EM structure of apo-form human DNA polymerase delta
6TNZ 4.05 Å, Human polymerase delta-FEN1-PCNA toolbelt
6S1M 4.27 Å, Human polymerase delta holoenzyme Conformer 1
6S1O 8.1 Å, Human polymerase delta holoenzyme Conformer 3

Browse structure collections

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