9OYG: E. coli clamp loader DnaX-complex alone

Structure of the E. coli clamp loader DnaX-complex alone. Determined by electron microscopy at 2.95 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 2.95 Å
Organism: Escherichia coli
Chains: 6
Atoms: 14,113
Mol. weight: 294.53 kDa
Ligands: ZN, AGS, MG, ADP
Released: 29 Apr 2026

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

Secondary structure: helices and β-sheets

9OYG contains 115 α-helices and 41 β-strands across 6 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	6-12	7
β-strand	20-24	5	2
β-strand	25	1	3
α-helix	28-45	18
β-strand	49-54	6	2
α-helix	61-68	8
β-strand	78-83	6	2
α-helix	91-103	13
β-strand	109-114	6	2
α-helix	119-122	4
α-helix	125-129	5
β-strand	134-136	3	2
β-strand	137	1	1
β-strand	139	1	3
α-helix	141-143	3
α-helix	147-157	11
β-strand	161-162	2	4
α-helix	164-173	10
α-helix	178-191	14
β-strand	196-197	2	4
α-helix	199-207	9
α-helix	214-223	10
α-helix	226-238	13
α-helix	243-264	22
α-helix	269-275	7
α-helix	280-292	13
α-helix	295-310	16
α-helix	311-315	5
α-helix	320-331	12
α-helix	339-342	4

Chain B: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-44	5	5
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-93	4	5
α-helix	104-107	4
α-helix	110-112	3
β-strand	121-126	6	5
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	5
α-helix	164-167	4
β-strand	171-173	3	5
α-helix	175-179	5
α-helix	180-193	14
β-strand	198	1	6
α-helix	200-210	11
α-helix	214-227	14
β-strand	232	1	6
α-helix	234-241	8
α-helix	249-258	10
α-helix	261-274	14
α-helix	278-297	20
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	363-365	3

Chain C: 23 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-45	6	8
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	8
α-helix	101-109	9
α-helix	114-115	2
β-strand	121-126	6	8
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-155	6	8
α-helix	164-167	4
β-strand	171-175	5	8
α-helix	176-179	4
α-helix	180-193	14
α-helix	200-209	10
α-helix	214-227	14
α-helix	234-241	8
α-helix	246-258	13
α-helix	261-273	13
α-helix	278-297	20
α-helix	304-306	3
α-helix	310-317	8
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
α-helix	364-368	5

Chain D: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-44	5	9
α-helix	51-62	12
α-helix	77-84	8
α-helix	103-112	10
α-helix	114-115	2
β-strand	123	1	9
β-strand	126	1	9
α-helix	128-130	3
α-helix	133-144	12
β-strand	152-156	5	9
α-helix	159-161	3
α-helix	164-169	6
β-strand	173-174	2	9
α-helix	176-178	3
α-helix	180-193	14
β-strand	198	1	10
α-helix	200-209	10
α-helix	214-227	14
β-strand	232	1	10
α-helix	234-241	8
α-helix	246-257	12
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	345-356	12

Chain E: 22 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	26-30	5	11
α-helix	37-49	13
β-strand	54	1	12
β-strand	57	1	12
α-helix	63-69	7
β-strand	76-78	3	11
α-helix	80-82	3
β-strand	88	1	13
α-helix	90-101	12
α-helix	103-104	2
β-strand	110-114	5	11
α-helix	117-119	3
β-strand	120	1	13
α-helix	122-133	12
β-strand	139-145	7	11
α-helix	148-150	3
α-helix	153-158	6
β-strand	160-163	4	11
α-helix	165-168	4
α-helix	169-177	9
α-helix	184-193	10
α-helix	198-205	8
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	329-332	4

Chain J: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-12	9
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)
DNA polymerase III subunit psi	J	protein	30	Escherichia coli	P28632 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OYG_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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

>9OYG_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

>9OYG_3 DNA polymerase III subunit delta' (chains E)
MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG
HCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL
TDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV
TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ
APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQL
MSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Sequence of entity 4 (J), FASTA

>9OYG_4 DNA polymerase III subunit psi (chains J)
SRRDWQLQQLGITQWSLRRPGALQGEIAIA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

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…
9OYI 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…

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