1JQL: DNA Polymerase III, BETA CHAIN

Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of beta-delta (1-140). Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Sept 2001.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Escherichia coli
Chains: 2
Atoms: 3,932
Mol. weight: 56.11 kDa
Released: 26 Sept 2001

Explore 1JQL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1JQL contains 23 α-helices and 33 β-strands across 2 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: 15 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	7-17	11
α-helix	29-31	3
β-strand	32-38	7	2
β-strand	41-47	7	2
β-strand	51-58	8	2
β-strand	64	1	1
β-strand	66-71	6	2
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	1
β-strand	96-101	6	1
β-strand	104-109	6	1
α-helix	113-115	3
α-helix	118-120	3
β-strand	126-131	6	2
α-helix	132-140	9
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-172	16	3
β-strand	176-196	21	3
α-helix	197-205	9
β-strand	213-218	6	2
β-strand	222-227	6	2
β-strand	230-235	6	2
α-helix	236	1
β-strand	237	1	3
α-helix	244-246	3
β-strand	254-259	6	3
α-helix	260-273	14
β-strand	281-286	6	4
β-strand	289-294	6	4
β-strand	304-307	4	4
β-strand	309	1	3
β-strand	315-319	5	4
α-helix	321-330	10
β-strand	335-340	6	3
β-strand	347-351	5	3
β-strand	357-361	5	3
α-helix	362-363	2
β-strand	364	1	4

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	5
α-helix	6-8	3
α-helix	9-15	7
β-strand	20-24	5	5
α-helix	28-44	17
β-strand	49-51	3	6
α-helix	61-69	9
β-strand	78-80	3	6
β-strand	81-83	3	5
α-helix	93-103	11
β-strand	110-113	4	5
α-helix	121-123	3
α-helix	125-130	6
α-helix	131-133	3
β-strand	135-138	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA Polymerase III, BETA CHAIN	A	protein	366	Escherichia coli	P0A988 (AlphaFold model)
DNA Polymerase III, DELTA SUBUNIT	B	protein	140	Escherichia coli	P28630 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1JQL_1 DNA Polymerase III, BETA CHAIN (chains A)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAAASNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Sequence of entity 2 (B), FASTA

>1JQL_2 DNA Polymerase III, DELTA SUBUNIT (chains B)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQ

Primary citation

Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Jeruzalmi, D., Yurieva, O., Zhao, Y. et al. Cell (2001) 106:417-428. DOI 10.1016/S0092-8674(01)00462-7 · PubMed

Other PDB entries of the same protein (UniProt P0A988 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAY 1.21 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.
8PAT 1.45 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3.
4K3L 1.5 Å, E. coli sliding clamp in complex with AcLF dipeptide
8CIY 1.54 Å, DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with…
7AZ8 1.61 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound
4MJR 1.62 Å, E. coli sliding clamp in complex with (S)-Carprofen
6FVM 1.63 Å, Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
3D1G 1.64 Å, Structure of a small molecule inhibitor bound to a DNA sliding clamp
1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
7AZ7 1.65 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 37 bound
4N96 1.7 Å, E. coli sliding clamp in complex with 6-nitroindazole
4N98 1.7 Å, E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid

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