8VAQ: E. coli clamp loader

Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA1 conformation. Determined by electron microscopy at 3.8 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Escherichia coli, synthetic construct
Chains: 9
Atoms: 20,779
Mol. weight: 300.4 kDa
Ligands: MG, ADP, ZN, BEF
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8VAQ contains 140 α-helices and 84 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: 20 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-13	8
β-strand	20-25	6	1
α-helix	28-45	18
β-strand	47-54	8	1
α-helix	63-66	4
α-helix	71-73	3
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	134-139	6	1
α-helix	141-143	3
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	199-202	4
α-helix	214-223	10
α-helix	226-239	14
α-helix	243-264	22
α-helix	269-275	7
α-helix	280-292	13
α-helix	295-313	19
α-helix	320-330	11

Chain B: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-45	6	3
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	3
α-helix	101-108	8
α-helix	109-112	4
α-helix	114-115	2
β-strand	121-126	6	3
α-helix	133-144	12
β-strand	150-155	6	3
α-helix	164-167	4
β-strand	171-175	5	3
α-helix	176-179	4
α-helix	180-193	14
β-strand	198	1	4
α-helix	200-209	10
α-helix	214-227	14
β-strand	232	1	4
α-helix	234-243	10
α-helix	248-257	10
α-helix	261-273	13
α-helix	278-297	20
α-helix	299-302	4
α-helix	305-308	4
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-357	13

Chain C: 27 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-33	12
β-strand	40-45	6	5
α-helix	53-62	10
α-helix	77-84	8
β-strand	90-94	5	5
α-helix	101-109	9
β-strand	121-126	6	5
α-helix	128-130	3
α-helix	133-138	6
α-helix	140-144	5
β-strand	150-156	7	5
α-helix	159-161	3
α-helix	164-169	6
β-strand	171-175	5	5
α-helix	176-177	2
β-strand	178	1	6
α-helix	179	1
α-helix	180-193	14
β-strand	198	1	7
α-helix	200-209	10
β-strand	212	1	6
α-helix	214-227	14
β-strand	232	1	7
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	304-309	6
α-helix	310-317	8
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-359	15
α-helix	364-368	5

Chain D: 24 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-33	12
β-strand	40-45	6	8
α-helix	51-63	13
α-helix	77-83	7
β-strand	91-94	4	8
α-helix	101-110	10
α-helix	114-115	2
β-strand	121-126	6	8
α-helix	128-130	3
α-helix	133-138	6
α-helix	141-144	4
β-strand	150-156	7	8
α-helix	159-161	3
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	248-257	10
α-helix	261-274	14
α-helix	278-297	20
α-helix	299-302	4
α-helix	310-319	10
α-helix	322-337	16
α-helix	345-359	15

Chain E: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-19	12
β-strand	26-30	5	9
α-helix	37-48	12
α-helix	63-69	7
β-strand	76-79	4	9
β-strand	88	1	10
α-helix	90-101	12
β-strand	110-114	5	9
α-helix	117-119	3
β-strand	120	1	10
α-helix	122-126	5
α-helix	129-133	5
β-strand	139-145	7	9
α-helix	153-156	4
β-strand	160-163	4	9
α-helix	165-168	4
α-helix	169-179	11
α-helix	184-193	10
α-helix	198-206	9
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	308-323	16
α-helix	328-330	3

Chain F: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	8-17	10
α-helix	28-31	4
β-strand	32-38	7	12
β-strand	41-47	7	12
β-strand	51-58	8	12
β-strand	66-71	6	12
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	11
β-strand	96-101	6	11
β-strand	104-109	6	11
β-strand	111	1	12
α-helix	119-121	3
β-strand	124-130	7	12
α-helix	132-140	9
α-helix	143-145	3
β-strand	158-172	15	13
β-strand	176-195	20	13
α-helix	197-206	10
β-strand	214-219	6	12
β-strand	222-227	6	12
β-strand	230-235	6	12
α-helix	244-247	4
β-strand	256-259	4	13
α-helix	260-273	14
β-strand	281-285	5	14
β-strand	290-295	6	14
β-strand	301-304	4	14
β-strand	309	1	13
β-strand	315-319	5	14
α-helix	321-331	11
β-strand	335-340	6	13
β-strand	347-351	5	13
β-strand	354-361	8	13
α-helix	363-365	3

Chain G: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
α-helix	7-9	3
α-helix	11-18	8
α-helix	28-30	3
β-strand	34-38	5	15
β-strand	41-47	7	15
β-strand	51-58	8	15
β-strand	66-68	3	15
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	14
β-strand	96-101	6	14
β-strand	104-109	6	14
α-helix	113-115	3
β-strand	126-130	5	15
α-helix	132-142	11
α-helix	153-156	4
β-strand	157-172	16	16
β-strand	176-188	13	16
β-strand	193-196	4	16
α-helix	197-206	10
α-helix	213	1
β-strand	214-218	5	15
β-strand	222-227	6	15
β-strand	230-235	6	15
α-helix	244-247	4
β-strand	254-259	6	16
α-helix	260-270	11
α-helix	271-273	3
β-strand	280-286	7	11
β-strand	289-295	7	11
β-strand	301-307	7	11
β-strand	309	1	16
β-strand	315-320	6	11
α-helix	321-330	10
β-strand	335-340	6	16
β-strand	347-351	5	16
β-strand	357-361	5	16

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	376	Escherichia coli	P06710 (AlphaFold model)
DNA polymerase III subunit delta'	E	protein	337	Escherichia coli	P28631 (AlphaFold model)
Beta sliding clamp	F, G	protein	369	Escherichia coli	P0A988 (AlphaFold model)
DNA (5'-d(pgpcpapgpapcpapcptpapcpgpapgptpapcpaptpa)-3')	H	DNA	20	synthetic construct
DNA (27-mer)	I	DNA	30	synthetic construct

Sequence of entity 1 (A), FASTA

>8VAQ_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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

>8VAQ_2 DNA polymerase III subunit tau (chains B, C, D)
GPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARL
LAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR
GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKA
LDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV
SAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQL
SPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRAL
AFHPRMPLPEPEVPRQ

Sequence of entity 3 (E), FASTA

>8VAQ_3 DNA polymerase III subunit delta' (chains E)
GPHMRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHK
SCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDA
ALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLS
REVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALN
HEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIR
EQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Sequence of entity 4 (F, G), FASTA

>8VAQ_4 Beta sliding clamp (chains F, G)
GPHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARV
ALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFP
NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRL
AVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLV
DGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNP
EQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSA
AYVVMPMRL

Sequence of entity 5 (H), FASTA

>8VAQ_5 DNA (5'-D(P*GP*CP*AP*GP*AP*CP*AP*CP*TP*AP*CP*GP*AP*GP*TP*AP*CP*AP*TP*A)-3') (chains H)
GCAGACACTACGAGTACATA

Sequence of entity 6 (I), FASTA

>8VAQ_6 DNA (27-MER) (chains I)
TTTTTTTTTTTATGTACTCGTAGTGTCTGC

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
BEF	Beryllium trifluoride ion	Be F3	3

Primary citation

Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. Landeck, J.T., Pajak, J., Norman, E.K. et al. J Biol Chem (2024) 300:107166-107166. DOI 10.1016/j.jbc.2024.107166 · 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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