4HCC: Exodeoxyribonuclease I

The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA complex. Determined by X-ray diffraction at 2.96 Å resolution. Released 9 Oct 2013.

Method: X-ray diffraction
Resolution: 2.96 Å
Organism: Escherichia coli
Chains: 4
Atoms: 8,059
Mol. weight: 119.36 kDa
Ligands: ZN, PO4, IPA
Released: 9 Oct 2013

Explore 4HCC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HCC contains 63 α-helices and 25 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: 31 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	28-36	9	1
β-strand	42-50	9	1
β-strand	51	1	2
α-helix	61-67	7
α-helix	71-77	7
β-strand	79	1	2
α-helix	81-92	12
β-strand	97-101	5	1
α-helix	104-108	5
α-helix	109-118	10
α-helix	125-127	3
α-helix	129-131	3
β-strand	133-136	4	1
α-helix	137-147	11
α-helix	166-171	6
α-helix	183-200	18
α-helix	202-210	9
α-helix	214-218	5
β-strand	229-232	4	3
α-helix	234-236	3
α-helix	238-240	3
β-strand	243-251	9	3
β-strand	258-263	6	3
α-helix	269-273	5
α-helix	276-283	8
α-helix	293-296	4
β-strand	298-302	5	3
β-strand	308-311	4	3
α-helix	312-314	3
α-helix	317-323	7
α-helix	327-338	12
α-helix	342-351	10
α-helix	363-365	3
α-helix	367-369	3
α-helix	371-373	3
α-helix	374-384	11
α-helix	388-390	3
α-helix	401-414	14
α-helix	416-418	3
α-helix	421-434	14
α-helix	437-453	17
α-helix	458-474	17

Chain B: 32 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	4
β-strand	28-36	9	4
β-strand	42-52	11	4
α-helix	53-54	2
α-helix	61-67	7
α-helix	71-77	7
β-strand	78-80	3	4
α-helix	81-92	12
β-strand	97-101	5	4
α-helix	104-108	5
α-helix	109-118	10
α-helix	125-127	3
α-helix	129-131	3
β-strand	133-136	4	4
α-helix	137-147	11
β-strand	156	1	5
β-strand	162	1	5
α-helix	166-171	6
α-helix	183-200	18
α-helix	202-210	9
α-helix	214-218	5
β-strand	229-232	4	6
α-helix	234-236	3
α-helix	238-240	3
β-strand	243-251	9	6
β-strand	258-263	6	6
α-helix	269-273	5
α-helix	276-283	8
α-helix	287-289	3
α-helix	294-296	3
β-strand	298-302	5	6
β-strand	308-311	4	6
α-helix	312-314	3
α-helix	317-323	7
α-helix	327-339	13
α-helix	342-351	10
α-helix	363-365	3
α-helix	367-369	3
α-helix	374-384	11
α-helix	388-393	6
α-helix	402-414	13
α-helix	416-418	3
α-helix	421-434	14
α-helix	437-453	17
α-helix	458-475	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exodeoxyribonuclease I	A, B	protein	481	Escherichia coli	P04995 (AlphaFold model)
DNA (5'-d(apapapapapapapapapapapa)-3')	C, D	DNA	12

Sequence of entity 1 (A, B), FASTA

>4HCC_1 Exodeoxyribonuclease I (chains A, B)
MMNDGKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQ
PGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNF
YDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNA
HDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWR
GNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKL
VHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPS
DNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLD
YAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVHHHHH
H

Sequence of entity 2 (C, D), FASTA

>4HCC_2 DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') (chains C, D)
AAAAAAAAAAAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
PO4	Phosphate ion	O4 P	2
IPA	Isopropyl alcohol	C3 H8 O	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

The structures of Escherichia coli exonuclease I in complex with the single strand DNA. Qiu, R., Lou, T., Wei, J. et al. To be published.

Other PDB entries of the same protein (UniProt P04995 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QXF 1.5 Å, Product bound structure of exonuclease I at 1.5 angstrom resolution
3HL8 1.55 Å, Crystal structure of exonuclease I in complex with inhibitor BCBP
3HP9 1.6 Å, Crystal structure of SSB/Exonuclease I in complex with inhibitor CFAM
3C95 1.7 Å, Exonuclease I (apo)
4JRP 1.95 Å, Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide
4HCB 2.0 Å, The metal-free form of crystal structure of E.coli ExoI-ssDNA complex
1FXX 2.4 Å, The structure of exonuclease I suggests how processivity is achieved
3C94 2.7 Å, ExoI/SSB-Ct complex
4JRQ 3.0 Å, Crystal structure of E. coli Exonuclease I in complex with a 5cy-dA13 oligonucleotide
4JS4 3.1 Å, Crystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotide
4JS5 3.5 Å, Crystal structure of E. coli Exonuclease I in complex with a dT13 oligonucleotide

Browse structure collections

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