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- PDB-1rdh: CRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H DOMAI... -

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Basic information

Entry
Database: PDB / ID: 1rdh
TitleCRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H DOMAIN SHOW STRUCTURAL FEATURES THAT DISTINGUISH IT FROM THE INACTIVE FORM
ComponentsHIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN)
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsFinzel, B.C. / Chattopadhyay, D. / Einspahr, H.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form.
Authors: Chattopadhyay, D. / Finzel, B.C. / Munson, S.H. / Evans, D.B. / Sharma, S.K. / Strakalaitus, N.A. / Brunner, D.P. / Eckenrode, F.M. / Dauter, Z. / Betzel, C. / Einspahr, H.M.
#1: Journal: Science / Year: 1991
Title: Crystal Structure of the Ribonuclease H Domain of HIV-1 Reverse Transcriptase
Authors: Davies II, J.F. / Hostomska, Z. / Hostomsky, Z. / Jordan, S.R. / Matthews, D.A.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: A Recombinant Ribonuclease H Domain of HIV-1 Reverse Transcriptase that is Enzymatically Active
Authors: Evans, D.B. / Brawn, K. / Deibel Junior, M.R. / Tarpley, W.G. / Sharma, S.K.
History
DepositionMar 5, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN)
B: HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN)


Theoretical massNumber of molelcules
Total (without water)32,3932
Polymers32,3932
Non-polymers00
Water00
1
A: HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN)


Theoretical massNumber of molelcules
Total (without water)16,1961
Polymers16,1961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN)


Theoretical massNumber of molelcules
Total (without water)16,1961
Polymers16,1961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.030, 52.030, 113.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsTHERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THEY HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. THE RESIDUE NUMBERING IS BASED ON THE REVERSE TRANSCRIPTASE SEQUENCE.

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN) / Coordinate model: Cα atoms only


Mass: 16196.366 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
Sequence detailsTHIS RECOMBINANT VERSION OF THE HIV-1 RNASE H DOMAIN WAS PREPARED WITH AN N-TERMINAL SEQUENCE TO ...THIS RECOMBINANT VERSION OF THE HIV-1 RNASE H DOMAIN WAS PREPARED WITH AN N-TERMINAL SEQUENCE TO SIMPLIFY ISOLATION. THIS SEQUENCE MET-PRO-ILE-HIS-ASP-HIS-ASP-HIS-PRO-PHE-HIS -GLY PRECEDING TYR 427 IS COMPLETELY DISORDERED IN THE CRYSTAL AND NOT INCLUDED IN THIS ENTRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.5-10 mg/mlprotein1drop
220-23 %(w/v)PEG60001reservoir
30.1 Msodium citrate1reservoir
40.15 Msodium tartrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 8145 / % possible obs: 95 % / Num. measured all: 19985 / Rmerge(I) obs: 0.072

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→20 Å / σ(F): 2 /
RfactorNum. reflection
obs0.215 8147
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms254 0 0 0 254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.03
X-RAY DIFFRACTIONp_angle_d0.0520.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9951.5
X-RAY DIFFRACTIONp_mcangle_it1.6993
X-RAY DIFFRACTIONp_scbond_it1.7632
X-RAY DIFFRACTIONp_scangle_it2.8994
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.3830.3
X-RAY DIFFRACTIONp_singtor_nbd0.2290.4
X-RAY DIFFRACTIONp_multtor_nbd0.2640.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2490.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.53
X-RAY DIFFRACTIONp_staggered_tor10.85
X-RAY DIFFRACTIONp_orthonormal_tor16.710
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS

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