8GJ1: DNA polymerase III subunit delta

E. coli clamp loader with open clamp on primed template DNA (form 2). Determined by electron microscopy at 3.0 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Escherichia coli K-12, Escherichia coli
Chains: 10
Atoms: 20,982
Mol. weight: 415.59 kDa
Ligands: MG, ADP, ZN, ALF
Released: 27 Mar 2024

Explore 8GJ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GJ1 contains 145 α-helices and 88 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: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-8	3
α-helix	9-15	7
β-strand	20-25	6	1
α-helix	28-45	18
β-strand	50-54	5	1
α-helix	61-69	9
β-strand	79-83	5	1
α-helix	91-102	12
β-strand	109-114	6	1
α-helix	116-117	2
α-helix	119-122	4
α-helix	125-131	7
β-strand	134-139	6	1
α-helix	147-157	11
β-strand	161-162	2	2
α-helix	164-173	10
α-helix	178-191	14
β-strand	196-197	2	2
α-helix	199-203	5
α-helix	214-223	10
α-helix	226-239	14
α-helix	243-263	21
α-helix	264-266	3
α-helix	269-276	8
α-helix	280-292	13
α-helix	300-310	11
α-helix	311-315	5
α-helix	320-331	12

Chain B: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-44	5	3
α-helix	51-62	12
α-helix	77-84	8
β-strand	91-94	4	3
α-helix	101-109	9
α-helix	110-112	3
α-helix	114-115	2
β-strand	121-126	6	3
α-helix	128-130	3
α-helix	133-143	11
β-strand	150-155	6	3
α-helix	159-161	3
α-helix	164-168	5
β-strand	171-174	4	3
α-helix	180-194	15
α-helix	200-210	11
α-helix	214-227	14
α-helix	234-244	11
α-helix	248-257	10
α-helix	262-273	12
α-helix	278-297	20
α-helix	299-301	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
β-strand	360-361	2	4

Chain C: 26 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-44	5	5
α-helix	51-62	12
α-helix	77-83	7
β-strand	90-94	5	5
α-helix	101-109	9
α-helix	114-115	2
β-strand	121-126	6	5
α-helix	128-130	3
α-helix	133-138	6
α-helix	140-144	5
β-strand	150-155	6	5
α-helix	159-161	3
α-helix	164-167	4
β-strand	171-174	4	5
α-helix	175-179	5
α-helix	180-194	15
α-helix	200-209	10
α-helix	214-228	15
α-helix	234-241	8
α-helix	246-257	12
α-helix	261-274	14
α-helix	278-297	20
α-helix	299-301	3
α-helix	304-306	3
α-helix	307-317	11
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
α-helix	364-368	5

Chain D: 23 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-45	6	6
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	6
α-helix	95-97	3
α-helix	101-108	8
β-strand	113	1	7
α-helix	114-115	2
β-strand	121-126	6	6
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	6
α-helix	164-167	4
β-strand	171-175	5	6
α-helix	176-179	4
α-helix	180-194	15
β-strand	198	1	8
α-helix	200-209	10
α-helix	214-227	14
β-strand	232	1	8
α-helix	234-241	8
α-helix	248-258	11
α-helix	261-274	14
α-helix	278-297	20
α-helix	299-301	3
α-helix	304-309	6
α-helix	310-319	10
α-helix	322-337	16
α-helix	345-357	13

Chain E: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-20	13
β-strand	26-30	5	9
α-helix	37-49	13
β-strand	54	1	10
β-strand	57	1	10
α-helix	63-70	8
β-strand	77-79	3	9
β-strand	88	1	11
α-helix	90-100	11
α-helix	103-104	2
β-strand	110-114	5	9
α-helix	117-119	3
β-strand	120	1	11
α-helix	122-133	12
α-helix	135-136	2
β-strand	139-145	7	9
α-helix	148-150	3
α-helix	153-157	5
β-strand	160-163	4	9
α-helix	164-166	3
α-helix	169-179	11
α-helix	184-193	10
α-helix	200-206	7
α-helix	209-226	18
α-helix	229-232	4
α-helix	233-236	4
α-helix	241-260	20
α-helix	271-280	10
α-helix	283-302	20
α-helix	308-322	15
α-helix	328-330	3

Chain F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-12	9
α-helix	14-16	3
β-strand	17-18	2	4
α-helix	22-24	3

Chain H: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
α-helix	7-17	11
α-helix	28-31	4
β-strand	32-38	7	13
β-strand	41-47	7	13
β-strand	51-58	8	13
β-strand	64	1	12
β-strand	66-71	6	13
α-helix	72-81	10
α-helix	83	1
α-helix	86	1
β-strand	87-93	7	12
β-strand	96-101	6	12
β-strand	104-109	6	12
α-helix	113-115	3
α-helix	119-121	3
β-strand	124-130	7	13
α-helix	132-141	10
α-helix	153-156	4
β-strand	158-172	15	14
β-strand	176-195	20	14
α-helix	197-206	10
β-strand	214-219	6	13
β-strand	222-227	6	13
β-strand	230-235	6	13
α-helix	241-243	3
β-strand	254-259	6	14
α-helix	260-273	14
β-strand	281-286	6	15
β-strand	289-294	6	15
β-strand	304-306	3	15
β-strand	309-310	2	14
β-strand	315-319	5	15
α-helix	321-330	10
β-strand	335-340	6	14
β-strand	347-351	5	14
β-strand	358-361	4	14
α-helix	362-365	4

Chain I: 12 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-10	4
α-helix	13-18	6
α-helix	28-31	4
β-strand	32-38	7	17
β-strand	41-47	7	17
β-strand	51-58	8	17
β-strand	63	1	16
β-strand	66-71	6	17
α-helix	72-81	10
β-strand	87-93	7	16
β-strand	96-101	6	16
β-strand	104-109	6	16
α-helix	113-115	3
β-strand	126-130	5	17
α-helix	132-143	12
α-helix	153-155	3
β-strand	157-163	7	18
β-strand	166-172	7	18
β-strand	176-183	8	18
β-strand	191-196	6	18
α-helix	197-206	10
β-strand	214-218	5	17
β-strand	222-227	6	17
β-strand	230-235	6	17
α-helix	244-247	4
α-helix	249	1
β-strand	254-259	6	18
α-helix	260-270	11
β-strand	280-286	7	12
β-strand	289-294	6	12
β-strand	302-306	5	12
β-strand	309	1	18
β-strand	315-320	6	12
α-helix	321-331	11
β-strand	335-340	6	18
β-strand	347-351	5	18
β-strand	354-361	8	18
β-strand	364	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit delta	A	protein	343	Escherichia coli K-12	P28630 (AlphaFold model)
DNA polymerase III subunit tau	B, C, D	protein	643	Escherichia coli K-12	P06710 (AlphaFold model)
DNA polymerase III subunit delta'	E	protein	334	Escherichia coli K-12	P28631 (AlphaFold model)
DNA polymerase III subunit psi	F	protein	137	Escherichia coli K-12	P28632 (AlphaFold model)
Beta sliding clamp	H, I	protein	366	Escherichia coli K-12	P0A988
Primer	X	DNA	23	Escherichia coli
Template	Y	DNA	68	Escherichia coli

Sequence of entity 1 (A), FASTA

>8GJ1_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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

>8GJ1_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

>8GJ1_3 DNA polymerase III subunit delta' (chains E)
MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG
HCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL
TDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV
TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ
APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQL
MSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Sequence of entity 4 (F), FASTA

>8GJ1_4 DNA polymerase III subunit psi (chains F)
MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRA
LTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAA
LWQQICTYEHDFFPRND

Sequence of entity 5 (H, I), FASTA

>8GJ1_5 Beta sliding clamp (chains H, I)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Sequence of entity 6 (X), FASTA

>8GJ1_6 Primer (chains X)
GAGATAGTTACAACATACGATCG

Sequence of entity 7 (Y), FASTA

>8GJ1_7 Template (chains Y)
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGATCGTATGTTGTA
ACTATCTC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
ZN	Zinc ion	Zn	4
ALF	Tetrafluoroaluminate ion	Al F4	3

Primary citation

Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli. Xu, Z.Q., Jergic, S., Lo, A.T.Y. et al. Nat Commun (2024) 15:8372-8372. DOI 10.1038/s41467-024-52623-9 · 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…

Browse structure collections

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