1NJF: DNA polymerase III subunit gamma

Nucleotide bound form of an isolated E. coli clamp loader gamma subunit. Determined by X-ray diffraction at 2.3 Å resolution. Released 8 Apr 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Escherichia coli
Chains: 4
Atoms: 7,862
Mol. weight: 112.26 kDa
Ligands: ADP, AGS, ZN
Released: 8 Apr 2003

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

Secondary structure: helices and β-sheets

1NJF contains 60 α-helices and 28 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.

Chains A and B: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-33	12
β-strand	40-44	5	1
α-helix	51-63	13
α-helix	77-84	8
β-strand	90-94	5	1
α-helix	101-109	9
β-strand	121-126	6	1
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	1
α-helix	159-161	3
α-helix	164-167	4
β-strand	171-174	4	1
α-helix	175-179	5
α-helix	180-194	15
β-strand	198	1	2
α-helix	200-209	10
α-helix	214-227	14
β-strand	232	1	2
α-helix	234-241	8

Chain C: 15 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	5
α-helix	51-63	13
α-helix	77-83	7
β-strand	90-94	5	5
α-helix	102-109	8
β-strand	121-126	6	5
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	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
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

Chain D: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-33	12
β-strand	40-44	5	7
α-helix	51-63	13
α-helix	77-83	7
β-strand	90-94	5	7
α-helix	101-109	9
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	164-167	4
β-strand	171-174	4	7
α-helix	175-179	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit gamma	A, B, C, D	protein	250	Escherichia coli	P06710 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1NJF_1 DNA polymerase III subunit gamma (chains A, B, C, D)
GAHMGGSMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTS
IARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQY
APARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQF
HLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVS
TQAVSAMLGT

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	3
ZN	Zinc ion	Zn	4

Primary citation

Nucleotide-Induced Conformational Changes in an Isolated Escherichia coli DNA Polymerase III Clamp Loader Subunit. Podobnik, M., Weitze, T.F., O'Donnell, M. et al. Structure (2003) 11:253-263. DOI 10.1016/S0969-2126(03)00027-3 · PubMed

Other PDB entries of the same protein (UniProt P06710 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NJG 2.2 Å, Nucleotide-free form of an Isolated E. coli Clamp Loader Gamma Subunit
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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