9OYI: DNA polymerase III subunit delta

Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 1 with fully open clamp and unsettled DNA. Determined by electron microscopy at 2.54 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 2.54 Å
Organisms: Escherichia coli, DNA molecule
Chains: 10
Atoms: 20,794
Mol. weight: 409.34 kDa
Ligands: AGS, ZN, MG
Released: 29 Apr 2026

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

Secondary structure: helices and β-sheets

9OYI contains 150 α-helices and 99 β-strands across 8 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: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-8	3
α-helix	9-14	6
β-strand	20-24	5	1
α-helix	28-44	17
β-strand	47-54	8	1
α-helix	61-69	9
β-strand	70	1	2
α-helix	71-72	2
β-strand	77-83	7	1
α-helix	91-101	11
β-strand	108-114	7	1
α-helix	116-118	3
α-helix	119-122	4
α-helix	125-129	5
β-strand	134-138	5	1
α-helix	140-143	4
α-helix	147-157	11
β-strand	161-162	2	3
α-helix	164-173	10
α-helix	178-191	14
β-strand	196-197	2	3
α-helix	199-203	5
α-helix	214-223	10
α-helix	226-239	14
α-helix	243-263	21
α-helix	269-275	7
α-helix	280-282	3
α-helix	283-292	10
α-helix	295-314	20
α-helix	321-331	11
α-helix	339-342	4

Chain B: 27 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-45	6	4
α-helix	51-63	13
α-helix	77-84	8
β-strand	90-94	5	4
α-helix	101-109	9
α-helix	110-112	3
β-strand	113	1	5
α-helix	114-115	2
β-strand	121-126	6	4
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	4
α-helix	159-161	3
α-helix	164-168	5
β-strand	171-175	5	4
α-helix	176-179	4
α-helix	180-194	15
β-strand	198	1	6
α-helix	200-210	11
α-helix	214-228	15
β-strand	232	1	6
α-helix	234-243	10
α-helix	248-257	10
α-helix	261-273	13
α-helix	278-297	20
α-helix	299-301	3
α-helix	304-306	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
β-strand	359-361	3	7
α-helix	362-364	3

Chain C: 26 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-44	5	8
α-helix	51-63	13
α-helix	77-84	8
β-strand	90-94	5	8
α-helix	101-108	8
α-helix	114-115	2
β-strand	121-126	6	8
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	8
α-helix	159-161	3
α-helix	164-168	5
β-strand	171-174	4	8
α-helix	175-179	5
α-helix	180-194	15
β-strand	198	1	9
α-helix	200-210	11
α-helix	214-228	15
β-strand	232	1	9
α-helix	234-241	8
α-helix	246-258	13
α-helix	261-272	12
α-helix	278-297	20
α-helix	299-301	3
α-helix	304-306	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
α-helix	365-368	4

Chain D: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-44	5	10
α-helix	51-63	13
α-helix	77-84	8
β-strand	90-94	5	10
α-helix	101-110	10
β-strand	113	1	11
α-helix	114-115	2
β-strand	121-126	6	10
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	10
α-helix	159-161	3
α-helix	164-169	6
β-strand	171-174	4	10
α-helix	175-179	5
α-helix	180-194	15
β-strand	198	1	12
α-helix	200-210	11
α-helix	214-227	14
β-strand	232	1	12
α-helix	234-241	8
α-helix	246-258	13
α-helix	261-273	13
α-helix	278-297	20
α-helix	299-301	3
α-helix	304-306	3
α-helix	310-319	10
α-helix	322-337	16
α-helix	339-341	3
α-helix	345-357	13

Chain E: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	26-30	5	13
α-helix	37-48	12
β-strand	54	1	14
β-strand	57	1	14
α-helix	63-70	8
β-strand	76-79	4	13
β-strand	88	1	15
α-helix	90-99	10
β-strand	102	1	16
β-strand	110-114	5	13
α-helix	117-119	3
β-strand	120	1	15
α-helix	122-133	12
α-helix	135-136	2
β-strand	139-145	7	13
α-helix	148-150	3
α-helix	153-158	6
β-strand	160-163	4	13
α-helix	165-168	4
α-helix	169-177	9
α-helix	184-193	10
α-helix	198-203	6
α-helix	209-226	18
α-helix	229-232	4
α-helix	233-236	4
α-helix	241-259	19
α-helix	271-280	10
α-helix	283-302	20
α-helix	308-322	15
α-helix	327-330	4

Chain F: 14 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
α-helix	7-17	11
α-helix	28-31	4
β-strand	32-38	7	18
β-strand	41-47	7	18
β-strand	51-58	8	18
β-strand	64	1	17
β-strand	66-71	6	18
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	17
β-strand	96-101	6	17
β-strand	104-109	6	17
β-strand	111	1	18
α-helix	113-115	3
β-strand	126-130	5	18
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-155	3
β-strand	158-172	15	5
β-strand	176-195	20	5
α-helix	197-206	10
α-helix	213	1
β-strand	214-218	5	18
β-strand	222-227	6	18
β-strand	230-235	6	18
α-helix	236	1
β-strand	237	1	5
β-strand	254-258	5	5
α-helix	260-273	14
β-strand	280-286	7	19
β-strand	289-294	6	19
β-strand	303-307	5	19
β-strand	309-310	2	5
β-strand	315-320	6	19
α-helix	321-331	11
β-strand	336-340	5	5
β-strand	347-349	3	5
β-strand	357-361	5	5
α-helix	362-363	2
β-strand	364	1	2

Chain G: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	20
α-helix	7-17	11
α-helix	30-32	3
β-strand	34-38	5	21
β-strand	41-47	7	21
β-strand	51-58	8	21
β-strand	64	1	20
β-strand	66-68	3	21
β-strand	69	1	22
α-helix	72-80	9
β-strand	87-92	6	20
β-strand	97-101	5	20
β-strand	104-106	3	20
β-strand	111	1	22
β-strand	126-130	5	21
α-helix	132-143	12
α-helix	153-155	3
β-strand	157-172	16	23
β-strand	176-196	21	23
α-helix	197-206	10
α-helix	213	1
β-strand	214-218	5	21
β-strand	222-227	6	21
β-strand	230-235	6	21
α-helix	236	1
β-strand	237	1	16
α-helix	244-247	4
β-strand	254-259	6	23
α-helix	260-270	11
β-strand	280-286	7	17
β-strand	289-295	7	17
β-strand	301-306	6	17
β-strand	309	1	23
β-strand	315-320	6	17
α-helix	321-331	11
β-strand	335-340	6	23
α-helix	346	1
β-strand	347-351	5	23
β-strand	357-361	5	23
β-strand	364	1	11

Chain J: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	17-19	3	7
α-helix	22-24	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit delta	A	protein	343	Escherichia coli	P28630 (AlphaFold model)
DNA polymerase III subunit tau	B, C, D	protein	643	Escherichia coli	P06710 (AlphaFold model)
DNA polymerase III subunit delta'	E	protein	334	Escherichia coli	P28631 (AlphaFold model)
Beta sliding clamp	F, G	protein	366	Escherichia coli	P0A988 (AlphaFold model)
DNA polymerase III subunit psi	J	protein	137	Escherichia coli	P28632
10-nt gapped DNA template strand	H	DNA	50	DNA molecule
10-nt gapped DNA primer strand 1	I	NA-hybrid	20	DNA molecule

Sequence of entity 1 (A), FASTA

>9OYI_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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

>9OYI_2 DNA polymerase III subunit tau (chains B, C, D)
MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAK
GLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRF
KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDV
EQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAM
LGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPA
ALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFH
PRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQAPTVPLPETTSQVLAARQQLQ
RVQGATKAKKSEPAAATRARPVNNAALERLASVTDRVQARPVPSALEKAPAKKEAYRWKA
TTPVMQQKEVVATPKALKKALEHEKTPELAAKLAAEAIERDPWAAQVSQLSLPKLVEQVA
LNAWKEESDNAVCLHLRSSQRHLNNRGAQQKLAEALSMLKGSTVELTIVEDDNPAVRTPL
EWRQAIYEEKLAQARESIIADNNIQTLRRFFDAELDEESIRPI

Sequence of entity 3 (E), FASTA

>9OYI_3 DNA polymerase III subunit delta' (chains E)
MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG
HCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL
TDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV
TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ
APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQL
MSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Sequence of entity 4 (F, G), FASTA

>9OYI_4 Beta sliding clamp (chains F, G)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Sequence of entity 5 (J), FASTA

>9OYI_5 DNA polymerase III subunit psi (chains J)
MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRA
LTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAA
LWQQICTYEHDFFPRND

Sequence of entity 6 (H), FASTA

>9OYI_6 10-nt gapped DNA template strand (chains H)
CGGTATAGGCGATACGAATCTTTTTTTTTTCCGTATAGCCGTAGCGAGCC

Sequence of entity 7 (I), FASTA

>9OYI_7 10-nt gapped DNA primer strand 1 (chains I)
GGCTCGCTACGGCTATACGG

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	3
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	3

Primary citation

The E. coli DnaX clamp loader sharply bends DNA to load beta-clamp at nicks and small gaps. Zheng, F., Yao, N.Y., Georgescu, R.E. et al. bioRxiv (2026). DOI 10.64898/2026.01.17.700081 · PubMed

Other PDB entries of the same protein (UniProt P28630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JQL 2.5 Å, Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader…
9OYJ 2.53 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYH 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
8GJ2 2.6 Å, E. coli clamp loader with closed clamp on primed template DNA
9OYK 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYM 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
1JR3 2.7 Å, Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA…
8GIZ 2.7 Å, E. coli clamp loader with open clamp
9OYN 2.7 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYC 2.71 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…
9OYE 2.72 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…
9OYD 2.73 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…

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