8VAM: E. coli clamp loader

Name: PDB 8VAM: Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation
Published: 2024-03-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation. Determined by electron microscopy at 3.9 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Escherichia coli
Chains: 7
Atoms: 18,771
Mol. weight: 284.03 kDa
Ligands: ZN, ADP, MG, BEF
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8VAM contains 129 α-helices and 91 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: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-15	10
β-strand	20-24	5	1
α-helix	28-44	17
β-strand	47-54	8	1
α-helix	61-63	3
α-helix	65-70	6
β-strand	77-83	7	1
α-helix	91-100	10
β-strand	108-114	7	1
α-helix	119-122	4
α-helix	125-129	5
β-strand	134-138	5	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	199-204	6
α-helix	215-223	9
α-helix	226-238	13
α-helix	243-261	19
α-helix	269-275	7
α-helix	280-292	13
α-helix	295-313	19
α-helix	320-331	12

Chain B: 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	3
α-helix	51-62	12
β-strand	64	1	4
β-strand	67	1	4
α-helix	77-84	8
β-strand	90-94	5	3
α-helix	101-110	10
α-helix	114-115	2
β-strand	121-126	6	3
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	3
α-helix	159-161	3
α-helix	164-169	6
β-strand	171-174	4	3
α-helix	175-179	5
α-helix	180-193	14
α-helix	200-210	11
α-helix	214-227	14
α-helix	234-237	4
α-helix	238-242	5
α-helix	250-258	9
α-helix	261-273	13
α-helix	278-295	18
α-helix	299-301	3
α-helix	304-306	3
α-helix	310-318	9
α-helix	322-338	17
α-helix	345-358	14
α-helix	364-366	3

Chain C: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-45	6	5
α-helix	51-62	12
α-helix	77-83	7
β-strand	90-94	5	5
α-helix	95-98	4
α-helix	101-109	9
β-strand	121-126	6	5
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-155	6	5
α-helix	164-168	5
β-strand	173-175	3	5
α-helix	176-179	4
α-helix	180-193	14
β-strand	198	1	6
α-helix	200-209	10
α-helix	214-227	14
β-strand	232	1	6
α-helix	234-241	8
α-helix	246-258	13
α-helix	261-273	13
α-helix	278-294	17
α-helix	299-301	3
α-helix	305-308	4
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
α-helix	364-366	3

Chain D: 20 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-44	5	7
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	7
α-helix	101-110	10
β-strand	113	1	8
β-strand	121-126	6	7
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	7
α-helix	159-161	3
α-helix	164-169	6
β-strand	171-174	4	7
α-helix	176-179	4
α-helix	180-193	14
α-helix	200-209	10
α-helix	214-226	13
α-helix	234-241	8
α-helix	246-257	12
α-helix	261-274	14
α-helix	278-297	20
α-helix	310-319	10
α-helix	322-337	16
α-helix	345-356	12

Chain E: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-19	12
β-strand	28-30	3	9
α-helix	37-49	13
α-helix	66-69	4
β-strand	77-79	3	10
β-strand	88	1	11
α-helix	90-100	11
β-strand	102	1	12
α-helix	103-104	2
β-strand	110-111	2	13
β-strand	112-114	3	10
β-strand	120	1	11
α-helix	122-133	12
β-strand	139-140	2	13
β-strand	143-145	3	9
α-helix	155-158	4
β-strand	163	1	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	230-236	7
α-helix	241-259	19
α-helix	271-280	10
α-helix	283-302	20
α-helix	308-323	16
α-helix	327-330	4

Chain F: 13 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	14
α-helix	8-17	10
β-strand	32-38	7	15
β-strand	41-47	7	15
β-strand	51-58	8	15
α-helix	59	1
β-strand	67-71	5	15
α-helix	72-81	10
α-helix	83	1
α-helix	86-87	2
β-strand	88-93	6	14
β-strand	96-101	6	14
β-strand	104-109	6	14
β-strand	111	1	15
β-strand	126	1	15
β-strand	131	1	16
α-helix	132-142	11
α-helix	153-155	3
β-strand	158-164	7	17
β-strand	166-173	8	17
β-strand	176-182	7	17
β-strand	188-195	8	17
α-helix	197-207	11
β-strand	213	1	16
β-strand	215-218	4	15
β-strand	222-227	6	15
β-strand	230-235	6	15
β-strand	237	1	17
α-helix	241-243	3
α-helix	244-247	4
β-strand	254-256	3	17
β-strand	259	1	18
α-helix	261-272	12
β-strand	281-286	6	19
β-strand	289-295	7	19
β-strand	301-306	6	19
β-strand	310	1	17
β-strand	315-319	5	19
α-helix	321-330	10
β-strand	335	1	18
β-strand	336-340	5	17
β-strand	342	1	20
β-strand	345	1	20
β-strand	347-351	5	17
β-strand	357-361	5	17
α-helix	362-363	2
β-strand	364	1	19

Chain G: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	120-124	5
β-strand	126-128	3	21
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-172	16	22
β-strand	177-191	15	22
β-strand	194-196	3	22
α-helix	197-206	10
β-strand	215-218	4	21
β-strand	222-227	6	21
β-strand	230-231	2	21
β-strand	234-235	2	21
β-strand	237	1	12
α-helix	241-243	3
β-strand	254-259	6	22
α-helix	260-270	11
α-helix	271-273	3
β-strand	280-285	6	14
β-strand	290-295	6	14
β-strand	301-306	6	14
β-strand	309-310	2	22
β-strand	315-320	6	14
α-helix	321-331	11
β-strand	335-340	6	22
β-strand	347-351	5	22
β-strand	357-361	5	22
β-strand	364	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit delta	A	protein	333	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)

Sequence of entity 1 (A), FASTA

>8VAM_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCH

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

>8VAM_2 DNA polymerase III subunit tau (chains B, C, D)
GPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARL
LAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR
GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKA
LDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV
SAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQL
SPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRAL
AFHPRMPLPEPEVPRQ

Sequence of entity 3 (E), FASTA

>8VAM_3 DNA polymerase III subunit delta' (chains E)
GPHMRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHK
SCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDA
ALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLS
REVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALN
HEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIR
EQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Sequence of entity 4 (F, G), FASTA

>8VAM_4 Beta sliding clamp (chains F, G)
GPHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARV
ALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFP
NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRL
AVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLV
DGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNP
EQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSA
AYVVMPMRL

Ligands and cofactors

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

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