5YV3: DNA polymerase IV - DNA ternary complex 7

DNA polymerase IV - DNA ternary complex 7. Determined by X-ray diffraction at 2.03 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Escherichia coli K-12
Chains: 6
Atoms: 7,230
Mol. weight: 102.99 kDa
Ligands: MG, TTP, DPO
Released: 7 Nov 2018

Explore 5YV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YV3 contains 38 α-helices and 36 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: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
α-helix	12-20	9
α-helix	22-24	3
β-strand	29-32	4	8
β-strand	40	1	9
β-strand	41-44	4	8
α-helix	46-49	4
β-strand	58	1	9
α-helix	59-65	7
α-helix	69	1
β-strand	70-72	3	8
α-helix	76-93	18
β-strand	97-101	5	7
β-strand	104-108	5	7
α-helix	115-117	3
α-helix	119-134	16
β-strand	138-143	6	7
α-helix	146-155	10
β-strand	161-163	3	7
α-helix	166-168	3
α-helix	169-174	6
β-strand	177	1	10
α-helix	178-180	3
α-helix	186-193	8
β-strand	199	1	10
α-helix	200-204	5
α-helix	208-215	8
α-helix	217-225	9
α-helix	232-234	3
β-strand	242-253	12	11
α-helix	256-277	22
β-strand	282	1	12
β-strand	285-292	8	11
β-strand	297-303	7	11
β-strand	306	1	12
α-helix	309-323	15
β-strand	329-337	9	11

Chain F: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	12-20	9
α-helix	22-24	3
β-strand	29-32	4	2
β-strand	40	1	3
β-strand	41-44	4	2
α-helix	46-49	4
β-strand	58	1	3
α-helix	59-65	7
β-strand	70-72	3	2
α-helix	76-91	16
β-strand	97-101	5	1
β-strand	104-108	5	1
α-helix	114-117	4
α-helix	119-134	16
β-strand	138-143	6	1
α-helix	146-153	8
β-strand	161-163	3	1
α-helix	166-168	3
α-helix	169-174	6
β-strand	177	1	4
α-helix	178-180	3
α-helix	186-194	9
β-strand	199	1	4
α-helix	200-204	5
α-helix	208-215	8
α-helix	217-225	9
α-helix	232-234	3
β-strand	242-253	12	5
α-helix	256-277	22
β-strand	282	1	6
β-strand	285-292	8	5
β-strand	297-303	7	5
β-strand	306	1	6
α-helix	309-323	15
β-strand	329-337	9	5
α-helix	338-339	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase IV	A, F	protein	352	Escherichia coli K-12	Q47155 (AlphaFold model)
DTN1	B, G	DNA	18	Escherichia coli K-12
DTN2	C, H	DNA	19	Escherichia coli K-12

Sequence of entity 1 (A, F), FASTA

>5YV3_1 DNA polymerase IV (chains A, F)
GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPT
GMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSA
TLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLA
KIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERL
RKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDPQMERQLVLGL

Sequence of entity 2 (B, G), FASTA

>5YV3_2 DTN1 (chains B, G)
TCTAGGGTCCTAGGACCC

Sequence of entity 3 (C, H), FASTA

>5YV3_3 DTN2 (chains C, H)
TCTAGGGTCCTAGGACCCT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
TTP	Thymidine-5'-triphosphate	C10 H17 N2 O14 P3	2
DPO	Diphosphate	O7 P2	1

Primary citation

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Kottur, J., Nair, D.T. Nucleic Acids Res (2018) 46:5875-5885. DOI 10.1093/nar/gky402 · PubMed

Other PDB entries of the same protein (UniProt Q47155 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
5YUY 1.74 Å, DNA polymerase IV - DNA ternary complex 9
5YUZ 1.83 Å, DNA polymerase IV - DNA ternary complex 11
5YUU 1.89 Å, DNA polymerase IV - DNA ternary complex 4
1UNN 1.9 Å, Complex of beta-clamp processivity factor and little finger domain of PolIV
5YV2 1.9 Å, DNA polymerase IV - DNA ternary complex 14
5YUS 1.94 Å, DNA polymerase IV - DNA ternary complex 2
6IG1 1.97 Å, DNA polymerase IV - DNA ternary complex 10
5YUR 2.04 Å, DNA polymerase IV - DNA ternary complex 1
5YUX 2.04 Å, DNA polymerase IV - DNA ternary complex 8
5YYD 2.05 Å, DNA polymerase IV - ternary complex 15
5YUV 2.06 Å, DNA polymerase IV - DNA ternary complex 5

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