1JQJ: 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 the beta-delta complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 7 Nov 2001.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 4
Atoms: 10,860
Mol. weight: 158.58 kDa
Released: 7 Nov 2001

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

Secondary structure: helices and β-sheets

1JQJ contains 54 α-helices and 77 β-strands across 4 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: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
α-helix	8-16	9
β-strand	32	1	2
β-strand	34-38	5	3
β-strand	41-47	7	3
β-strand	51-58	8	3
β-strand	63-64	2	1
β-strand	66-69	4	3
β-strand	71	1	2
α-helix	73-80	8
β-strand	88-93	6	1
β-strand	96-98	3	1
β-strand	101	1	4
β-strand	104	1	4
β-strand	107-109	3	1
β-strand	111-112	2	3
β-strand	124	1	3
β-strand	128-129	2	3
α-helix	132-140	9
α-helix	143-145	3
α-helix	153-156	4
β-strand	157-172	16	5
β-strand	176-196	21	5
α-helix	197-206	10
β-strand	215-219	5	3
β-strand	222-227	6	3
β-strand	230-235	6	3
β-strand	237	1	5
α-helix	244-246	3
β-strand	255-259	5	6
α-helix	260-273	14
α-helix	277-279	3
β-strand	281-286	6	7
β-strand	289-294	6	7
β-strand	303-304	2	7
β-strand	309-311	3	6
β-strand	315-319	5	7
α-helix	321-330	10
β-strand	335-339	5	6
β-strand	347	1	5
β-strand	350-351	2	6
β-strand	357-361	5	5
β-strand	364	1	7

Chain B: 10 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	8
α-helix	8-16	9
β-strand	32	1	9
β-strand	34-38	5	10
β-strand	41-47	7	10
β-strand	51-58	8	10
β-strand	63-64	2	8
β-strand	66-69	4	10
β-strand	71	1	9
α-helix	73-80	8
β-strand	88-93	6	8
β-strand	96-98	3	8
β-strand	101	1	11
β-strand	104	1	11
β-strand	107-109	3	8
β-strand	111-112	2	10
α-helix	122-123	2
β-strand	124-129	6	10
α-helix	132-140	9
β-strand	157-172	16	12
β-strand	176-196	21	12
α-helix	197-206	10
β-strand	215-219	5	10
β-strand	222-227	6	10
β-strand	230-235	6	10
α-helix	236	1
β-strand	237	1	12
α-helix	244-246	3
β-strand	255-259	5	13
α-helix	260-273	14
α-helix	277-279	3
β-strand	281-286	6	14
β-strand	289-294	6	14
β-strand	303-304	2	14
β-strand	309-311	3	13
β-strand	315-319	5	14
α-helix	321-330	10
β-strand	335-339	5	13
β-strand	347	1	12
β-strand	348-351	4	13
β-strand	357-361	5	12
β-strand	364	1	14

Chain C: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	15
α-helix	6-9	4
α-helix	11-13	3
β-strand	20-24	5	15
α-helix	28-43	16
β-strand	47-54	8	15
α-helix	61-68	8
β-strand	77-83	7	15
α-helix	93-100	8
β-strand	108-114	7	15
α-helix	121-123	3
α-helix	125-130	6
β-strand	135-138	4	15
α-helix	146-156	11
α-helix	164-174	11
α-helix	178-191	14
α-helix	199-206	8
α-helix	214-222	9
α-helix	226-235	10
α-helix	246-261	16
α-helix	283-292	10
α-helix	295-314	20
α-helix	325-331	7

Chain D: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	16
α-helix	6-9	4
β-strand	20-24	5	16
α-helix	28-43	16
β-strand	47-54	8	16
α-helix	61-68	8
β-strand	77-83	7	16
α-helix	93-100	8
β-strand	108-114	7	16
α-helix	121-123	3
α-helix	125-130	6
β-strand	135-138	4	16
α-helix	146-156	11
α-helix	164-174	11
α-helix	178-191	14
α-helix	199-206	8
α-helix	214-221	8
α-helix	226-239	14
α-helix	243-262	20
α-helix	272-274	3
α-helix	289-292	4
α-helix	295-314	20
α-helix	323-330	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III, beta chain	A, B	protein	366	Escherichia coli	P0A988 (AlphaFold model)
DNA polymerase III, delta subunit	C, D	protein	343	Escherichia coli	P28630 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1JQJ_1 DNA polymerase III, beta chain (chains A, B)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAAASNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Sequence of entity 2 (C, D), FASTA

>1JQJ_2 DNA polymerase III, delta subunit (chains C, D)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

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

Browse structure collections

About this viewer

MolViewer shows 1JQJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.