2YV0: Ribonuclease HI

Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations. Determined by X-ray diffraction at 1.4 Å resolution. Released 18 Mar 2008.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Escherichia coli
Chains: 1
Atoms: 1,451
Mol. weight: 17.56 kDa
Released: 18 Mar 2008

Explore 2YV0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YV0 contains 7 α-helices and 8 β-strands across 1 chain. 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 X: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	1
β-strand	18-28	11	1
β-strand	31-42	12	1
α-helix	44-57	14
β-strand	64-69	6	1
α-helix	72-76	5
α-helix	77-81	5
α-helix	82-87	6
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	128-142	15
β-strand	146	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease HI	X	protein	155	Escherichia coli	P0A7Y4 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>2YV0_1 Ribonuclease HI (chains X)
MLKQVEIFTDGSCLGNPGPGGYAAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK
EPCEVILSTDSQYLRQGITQWIHNWKKRGWKTADGKPVKNVDLWQRLDAALGQHQIKWEW
VKGHAGHPENERCHELARAAAMNPTLEDTGYQVEV

Primary citation

Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations. Haruki, M., Tanaka, M., Motegi, T. et al. FEBS J (2007) 274:5815-5825. DOI 10.1111/j.1742-4658.2007.06104.x · 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…
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…
7VSD 1.7 Å, E. coli Ribonuclease HI in complex with one Mg2+ (2)
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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