RNase H

HIV RNase H removes the original RNA template from the first DNA strand allowing synthesis of the complementary strand of DNA.

PDB-1o1w: HIV-1 (isolate UNKNOWN) RNase H - produced using SwissModel/SPDBV/POVray

Key web links:
ViralZone: HIV-1, HIV replication cycle, HIV resource
PDB: 1o1w (HIV-1 RNase H)
UniProt: P04585 (HIV-1 HXB2 POL)
Chime Tutorial:  not available
HIV-1/Human Protein Interaction DB: HIV-1 Pol
Los Alamos HIV structure DB: not available
EMBL: K03455 [EMBL/GenBank/DDBJ]


  • p15 (120 amino acids)

Cleavage sites:


  • Removes RNA template strand from RNA/DNA duplex.


  • Virion

RT Function & Host-Virus Protein Interactions:[TOP]

Genomic Location & Protein Sequence: [TOP]

HIV-1 (HXB2):

          10         20         30         40         50         60         70         80         90        100
| | | | | | | | | |
110 120
| |
[download in fasta format]

Length: 120 amino acids (residues 595 - 715)
Molecular Weight: 13167 Da
Theoretical pI: 6.8
Position relative to Pol protein: 596 - 715

Protein Domains/Folds/Motifs: [TOP]

InterPro signature for RNase H - IPR002156

Secondary Structure prediction:

Antigenic Sites - EMBOSS:

Predicted Motifs: Printer-friendly version

Protein kinase C:
Casein kinase II:
Tyrosine kinase:
cAMP / cGMP kinase:
Cell attachment motif:
Asp Protease motif:
Asp Prot Retro motif:
Cysteine-rich Region:
Tryptophan-rich Region:
Zinc-finger CCHC motif:
Leucine Zipper motif:

Primary and Secondary Database Entries: [TOP]


ViralZone: HIV-1, HIV replication cycle, HIV resource
PDB/MMDB: Search for HIV-1 & Ribonuclease H

UniProt: P04585 (HIV-1 HXB2 POL)
EMBL: K03455; AAB50259.1 [EMBL/GenBank/DDBJ]

InterPro: IPR002156
Pfam: PF00075
Prints: none
SCOP: SSF53098 RNase H-like protein
BLOCKS: P04585
Prosite: P04585
ProtoNet: P04585
Database of Interacting Proteins: P04585
ModBase: P04585
HIV-1/Human Protein Interaction DB: HIV-1 Pol
HIV-1 Sequence Database Los Alamos HIV Sequence Database

Reviews and References: [TOP]

Cite the resource by citing the following paper:
Doherty R et al. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology (2005), 9;2(1):18.

1 - HIV Sequence Compendium 2000
Kuiken CL, Foley B, Hahn B, Korber B, Marx PA, McCutchan F, Mellors JW, Mullins JI, Sodroski J, Wolinksy S.
Theoretical Biol. & Biophys. Group, Los Alamos Nat Lab, LA-UR 01-3860 [Read it online: Compendium]
2 - Retroviruses
Coffin JM, Hughes SH, Varmus HE.
CD-ROM ed. (2002) Cold Spring Harbor Laboratory Press [Read it online: NCBI Bookshelf]
3 - Molecular Characteristics of HIV-1 Subtype C Viruses from KwaZulu-Natal, South Africa:
Implications for Vaccine and Antiretroviral Control Strategies.
Gordon M, De Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S.
Journal of Virology 77(4): 2587-2599 (2003) [pubmed: 12551997]

Thanks to ViralZone at the Swiss Institute of Bioinformatics (SIB) for allowing the use of their images on bioafrica.net.
Page last updated by Megan Druce, Paula Sommer and Tulio de Oliveira (UKZN/Africa Centre) & Philippe Le Mercier, Chantal Hulo and Patrick Masson (SIB/ViralZone).