7VSD: E. coli Ribonuclease HI

E. coli Ribonuclease HI in complex with one Mg2+ (2). Determined by X-ray diffraction at 1.7 Å resolution. Released 2 Mar 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Escherichia coli (strain K12)
Chains: 2
Atoms: 2,668
Mol. weight: 35.51 kDa
Ligands: MG
Released: 2 Mar 2022

Explore 7VSD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VSD contains 16 α-helices and 16 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-13	11	1
β-strand	18-28	11	1
β-strand	31-42	12	1
α-helix	44-57	14
β-strand	63-69	7	1
α-helix	72-77	6
α-helix	78-82	5
α-helix	86-88	3
β-strand	91	1	2
β-strand	97	1	2
α-helix	98	1
α-helix	101-111	11
β-strand	115-120	6	1
α-helix	128-141	14
β-strand	146	1	1

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-13	11	3
β-strand	18-28	11	3
β-strand	31-42	12	3
α-helix	44-57	14
β-strand	63-69	7	3
α-helix	72-76	5
α-helix	77-81	5
α-helix	82-87	6
β-strand	91	1	4
β-strand	97	1	4
α-helix	98	1
α-helix	101-111	11
β-strand	115-120	6	3
α-helix	128-141	14
β-strand	146	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease HI	A, B	protein	155	Escherichia coli (strain K12)	P0A7Y4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7VSD_1 Ribonuclease HI (chains A, B)
MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK
EHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEW
VKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

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

Primary citation

Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography. Liao, Z., Oyama, T., Kitagawa, Y. et al. Acta Crystallogr D Struct Biol (2022) 78:390-398. DOI 10.1107/S2059798322000870 · PubMed

Other PDB entries of the same protein (UniProt P0A7Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JL1 1.3 Å, D10A E. coli ribonuclease HI
1F21 1.4 Å, Divalent metal cofactor binding in the kinetic folding trajectory of E. Coli…
2YV0 1.4 Å, Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple…
3QIO 1.4 Å, Crystal Structure of HIV-1 RNase H with engineered E. coli loop and N-hydroxy…
2RN2 1.48 Å, Structural details of ribonuclease H from escherichia coli as refined to an atomic…
1JXB 1.6 Å, I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI
3QIN 1.7 Å, Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol…
3HYF 1.7 Å, Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site…
1JL2 1.76 Å, Crystal structure of TCEO RNase H-a chimera combining the folding core from T.…
7VSA 1.76 Å, E. coli Ribonuclease HI in complex with two Mg2+
3AA4 1.79 Å, A52V E.coli RNase HI
1KVA 1.8 Å, E. Coli ribonuclease hi D134A mutant

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