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- PDB-1hni: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN A COMPLEX WITH THE NO... -

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Entry
Database: PDB / ID: 1hni
TitleSTRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN A COMPLEX WITH THE NONNUCLEOSIDE INHIBITOR ALPHA-APA R 95845 AT 2.8 ANGSTROMS RESOLUTION
Components
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
KeywordsNUCLEOTIDYLTRANSFERASE
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 / symbiont-mediated suppression of host gene expression / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AAA / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsDing, J. / Das, K. / Arnold, E.
Citation
Journal: Structure / Year: 1995
Title: Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution.
Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Jr., A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A. ...Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Jr., A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A.J. / Smith Jr., R.H. / Koepke, M.K. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#1: Journal: J.Mol.Recog. / Year: 1994
Title: Buried Surface Analysis of HIV-1 Reverse Transcriptase P66(Slash)P51 Heterodimer and its Interaction with DsDNA Template(Slash)Primer
Authors: Ding, J. / Jacobo-Molina, A. / Tantillo, C. / Lu, X. / Nanni, R.G. / Arnold, E.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase: Implications for Mechanisms of Drug Inhibition and Resistance
Authors: Tantillo, C. / Ding, J. / Jacobo-Molina, A. / Nanni, R.G. / Boyer, P.L. / Hughes, S.H. / Pauwels, R. / Andries, K. / Janssen, P.A.J. / Arnold, E.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 Angstroms Resolution Shows Bent DNA
Authors: Jacobo-Molina, A. / Ding, J. / Nanni, R.G. / Clark Junior, A.D. / Lu, X. / Tantillo, C. / Williams, R.L. / Kamer, G. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H. / Arnold, E.
#4: Journal: Perspect.Drug Discovery Des. / Year: 1993
Title: Review of HIV-1 Reverse Transcriptase Three-Dimensional Structure: Implications for Drug Design
Authors: Nanni, R.G. / Ding, J. / Jacobo-Molina, A. / Hughes, S.H. / Arnold, E.
#5: Journal: Nature / Year: 1992
Title: Structure of HIV-1 Reverse Transcriptase(Slash)DNA Complex at 7 Angstroms Resolution Showing Active Site Locations
Authors: Arnold, E. / Jacobo-Molina, A. / Nanni, R.G. / Williams, R.L. / Lu, X. / Ding, J. / Clark Junior, A.D. / Zhang, A. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H.
#6: Journal: J.Biol.Chem. / Year: 1992
Title: The Effects of Cysteine Mutations on the Reverse Transcriptases of Human Immunodeficiency Virus Types 1 and 2
Authors: Hizi, A. / Shaharabany, M. / Tal, R. / Hughes, S.H.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystals of a Ternary Complex of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with a Monoclonal Antibody Fab Fragment and Double-Stranded DNA Diffract X-Rays to 3.5 Angstroms Resolution
Authors: Jacobo-Molina, A. / Clark Junior, A.D. / Williams, R.L. / Nanni, R.G. / Clark, P. / Ferris, A.L. / Hughes, S.H. / Arnold, E.
#8: Journal: Aids Res.Hum.Retroviruses / Year: 1990
Title: HIV-1 Reverse Transcriptase Purified from a Recombinant Strain of Escherichia Coli
Authors: Clark, P.K. / Ferris, A.L. / Miller, D.A. / Hizi, A. / Kim, K.W. / Deringer-Boyer, S.M. / Mellini, M.L. / Clark Junior, A.D. / Arnold, G.F. / Lebherz III, W.B.
#9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Expression of Soluble, Enzymatically Active, Human Immunodeficiency Virus Reverse Transcriptase in Escherichia Coli and Analysis of Mutants
Authors: Hizi, A. / Mcgill, C. / Hughes, S.H.
History
DepositionFeb 28, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
B: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6243
Polymers114,1842
Non-polymers4401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-26 kcal/mol
Surface area47420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.300, 69.900, 106.500
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)


Mass: 64274.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)


Mass: 49909.277 Da / Num. of mol.: 1
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: P03367, RNA-directed DNA polymerase
#3: Chemical ChemComp-AAA / (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE


Mass: 440.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16Br2N2O2
Compound detailsTHE DEFINITION OF SECONDARY STRUCTURAL ELEMENTS IS LARGELY BASED ON PROGRAM PROCHECK AND HYDROGEN- ...THE DEFINITION OF SECONDARY STRUCTURAL ELEMENTS IS LARGELY BASED ON PROGRAM PROCHECK AND HYDROGEN-BONDING PATTERN. THE NAMES OF SECONDARY STRUCTURAL ELEMENTS WERE BASICALLY KEPT CONSISTENT WITH THAT USED BY THE AUTHORS IN JACOBO-MOLINA ET AL. (1993). SOME ASSIGNED BETA STRANDS DO NOT APPEAR TO PARTICIPATE IN BETA SHEETS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119-20 mg/mlprotein1drop
250 mMbis-Tris-propane1reservoir
3100 mMammonium sulfate1reservoir
410 %glycerol1reservoir
512 %(w/v)PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 30186 / % possible obs: 78.5 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.255 / Rfactor obs: 0.255 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 23 0 7815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 31444 / Rfactor Rfree: 0.36
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.24
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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