9EKB: Apo-form human DNA polymerase delta

Cryo-EM structure of apo-form human DNA polymerase delta. Determined by electron microscopy at 3.65 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.65 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,324
Mol. weight: 240.44 kDa
Ligands: SF4, ZN
Released: 5 Feb 2025

Explore 9EKB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EKB contains 77 α-helices and 74 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: 46 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	40-56	17
α-helix	81-84	4
β-strand	94-106	13	1
β-strand	122-131	10	1
β-strand	136-142	7	1
β-strand	147-151	5	2
α-helix	152-153	2
α-helix	158-174	17
β-strand	187-195	9	2
β-strand	196-197	2	3
β-strand	207-214	8	2
α-helix	220-228	9
β-strand	233	1	4
β-strand	237	1	4
β-strand	244	1	2
α-helix	250-258	9
β-strand	265-268	4	1
α-helix	269	1
β-strand	273-275	3	1
β-strand	282	1	5
β-strand	286-291	6	1
β-strand	296-298	3	1
α-helix	303-305	3
β-strand	311-319	9	6
α-helix	332-333	2
β-strand	334-343	10	6
β-strand	344	1	7
β-strand	346	1	7
β-strand	351-357	7	6
β-strand	368-371	4	6
α-helix	374-388	15
β-strand	392-395	4	6
α-helix	398-402	5
α-helix	403-413	11
β-strand	424	1	5
β-strand	431-438	8	8
β-strand	442-449	8	8
β-strand	455-458	4	6
α-helix	459-466	8
α-helix	474-482	9
α-helix	485-487	3
α-helix	491-498	8
α-helix	502-526	25
α-helix	528-539	12
α-helix	544-547	4
α-helix	552-566	15
β-strand	568-569	2	3
β-strand	571	1	2
α-helix	586	1
β-strand	587	1	9
α-helix	588	1
β-strand	592-594	3	10
β-strand	598-603	6	9
α-helix	606-613	8
β-strand	621	1	11
α-helix	627-630	4
β-strand	637-639	3	11
β-strand	645-647	3	11
α-helix	655-674	20
α-helix	680-704	25
α-helix	714-738	25
α-helix	741-743	3
β-strand	750-754	5	9
β-strand	759-762	4	9
α-helix	768-783	16
β-strand	792-798	7	9
β-strand	801-805	5	10
β-strand	808-812	5	10
β-strand	813-814	2	9
β-strand	824-826	3	10
α-helix	838-849	12
α-helix	850-854	5
α-helix	857-872	16
α-helix	878-881	4
β-strand	883-886	4	12
α-helix	891-893	3
α-helix	899-910	12
β-strand	921-924	4	12
β-strand	925-926	2	13
β-strand	927	1	14
α-helix	935-938	4
β-strand	939-940	2	13
α-helix	942-948	7
α-helix	950-951	2
β-strand	952	1	14
α-helix	954-957	4
α-helix	958-962	5
α-helix	963-974	12
α-helix	978-984	7
β-strand	1011	1	15
β-strand	1018	1	15
α-helix	1030-1032	3
α-helix	1033-1062	30
α-helix	1077-1096	20
α-helix	1100-1101	2

Chain B: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	10-11	2
β-strand	24-25	2	16
α-helix	26-29	4
β-strand	32-34	3	17
α-helix	37-39	3
α-helix	51-70	20
β-strand	79	1	18
α-helix	82-84	3
β-strand	91-100	10	18
α-helix	107-111	5
α-helix	119-122	4
β-strand	132-136	5	18
β-strand	141-146	6	18
β-strand	158-165	8	18
β-strand	171-177	7	18
α-helix	181-183	3
α-helix	185-189	5
β-strand	195-199	5	19
α-helix	209-222	14
α-helix	229-235	7
β-strand	238-244	7	19
α-helix	250-252	3
α-helix	272-287	16
β-strand	292-295	4	19
α-helix	308-312	5
α-helix	313-315	3
α-helix	319-321	3
β-strand	325-327	3	19
β-strand	334-336	3	17
β-strand	339-344	6	17
α-helix	347-354	8
α-helix	361-370	10
β-strand	401-407	7	17
β-strand	411-415	5	17
β-strand	423-429	7	17
α-helix	431-434	4
β-strand	436-441	6	19
β-strand	447-454	8	19

Chain C: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
β-strand	21	1	20
α-helix	23-30	8
α-helix	34-51	18
β-strand	60-69	10	19
β-strand	72-80	9	19
α-helix	85-91	7
β-strand	95-102	8	19
β-strand	103	1	20
α-helix	107-108	2
α-helix	112-124	13
α-helix	126-128	3
β-strand	135-136	2	16

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	40-54	15
α-helix	66-75	10
α-helix	82-90	9
α-helix	95-98	4

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	466	Homo sapiens	Q15054 (AlphaFold model)
DNA polymerase delta subunit 4	D	protein	114	Homo sapiens	Q9HCU8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EKB_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

>9EKB_2 DNA polymerase delta subunit 2 (chains B)
MFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHIYATRLIQ
MRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQ
PPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFAD
LAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSR
VILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFD
PTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMED
HLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPED
QTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP

Sequence of entity 3 (C), FASTA

>9EKB_3 DNA polymerase delta subunit 3 (chains C)
MADQLYLENIDEFVTDQNKIVTYKWLSYTLGVHVNQAKQMLYDYVERKRKENSGAQLHVT
YLVSGSLIQNGHSCHKVAVVREDKLEAVKSKLAVTASIHVYSIQKAMLKDSGPLFNTDYD
ILKSNLQNCSKFSAIQCAAAVPRAPAESSSSSKKFEQSHLHMSSETQANNELTTNGHGPP
ASKQVSQQPKGIMGMFASKAAAKTQETNKETKTEAKEVTNASAAGNKAPGKGNMMSNFFG
KAAMNKFKVNLDSEQAVKEEKIVEQPTVSVTEPKLATPAGLKKSSKKAEPVKVLQKEKKR
GKRVALSDDETKETENMRKKRRRIKLPESDSSEDEVFPDSPGAYEAESPSPPPPPSPPLE
PVPKTEPEPPSVKSSSGENKRKRKRVLKSKTYLDGEGCIVTEKVYESESCTDSEEELNMK
TSSVHRPPAMTVKKEPREERKGPKKGTAALGKANRQVSITGFFQRK

Sequence of entity 4 (D), FASTA

>9EKB_4 DNA polymerase delta subunit 4 (chains D)
MGRKRLITDSYPVVKRREGPAGHSKGELAPELGEEPQPRDEEEAELELLRQFDLAWQYGP
CTGITRLQRWCRAKQMGLEPPPEVWQVLKTHPGDPRFQCSLWHLYPLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
ZN	Zinc ion	Zn	1

Primary citation

Cryo-EM structure of apo-form human DNA polymerase delta elucidates its minimal DNA synthesis activity without PCNA. Shin, Y., Hedglin, M., Murakami, K.S. J Biol Chem (2025) 301:108342-108342. DOI 10.1016/j.jbc.2025.108342 · 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
6TNZ 4.05 Å, Human polymerase delta-FEN1-PCNA toolbelt
6S1M 4.27 Å, Human polymerase delta holoenzyme Conformer 1
6S1N 4.86 Å, Human polymerase delta holoenzyme Conformer 2
6S1O 8.1 Å, Human polymerase delta holoenzyme Conformer 3

Browse structure collections

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