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Open data
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Basic information
Entry | Database: PDB / ID: 2hmi | |||||||||
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Title | HIV-1 REVERSE TRANSCRIPTASE/FRAGMENT OF FAB 28/DNA COMPLEX | |||||||||
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![]() | IMMUNE SYSTEM/DNA / AIDS / HIV-1 / RT / POLYMERASE / IMMUNE SYSTEM-DNA COMPLEX | |||||||||
Function / homology | ![]() HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ding, J. / Arnold, E. | |||||||||
![]() | ![]() Title: Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution. Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E. #1: ![]() Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Junior, A.D. / Hughes, S.H. / Arnold, E. #2: ![]() Title: Crystallization of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with and without Nucleic Acid Substrates, Inhibitors, and an Antibody Fab Fragment Authors: Clark Junior, A.D. / Jacobo-Molina, A. / Clark, P. / Hughes, S.H. / Arnold, E. #3: ![]() 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 Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P. ...Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A.J. / Smith Junior, R.H. / Koepke, M.K. / Michejda, C.J. / Hughes, S.H. / Arnold, E. #4: ![]() Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A. / Hughes, S.H. / Arnold, E. #5: ![]() Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A 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. #6: ![]() Title: Structure of HIV-1 Reverse Transcriptase/DNA Complex at 7 A 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298.6 KB | Display | ![]() |
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PDB format | ![]() | 241.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.9 KB | Display | ![]() |
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Full document | ![]() | 565 KB | Display | |
Data in XML | ![]() | 59.8 KB | Display | |
Data in CIF | ![]() | 82.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules EF
#1: DNA chain | Mass: 5864.801 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5484.528 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 64274.652 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 50281.762 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Antibody , 2 types, 2 molecules CD
#5: Antibody | Mass: 22984.068 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Antibody | Mass: 23457.156 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Details
Compound details | HIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED AS P66 (CHAIN A) AND P51 ...HIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED |
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Sequence details | THE BOUND DOUBLE-STRANDED DNA IS A 19-MER/18-MER TEMPLATE- PRIMER. BOTH THE TEMPLATE STRAND AND THE ...THE BOUND DOUBLE-STRANDED DNA IS A 19-MER/18-MER TEMPLATE- PRIMER. BOTH THE TEMPLATE STRAND AND THE PRIMER STRAND ARE NUMBERED IN THE 5'-3' DIRECTION. THE FIRST NUCLEOTIDE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.29 Å3/Da / Density % sol: 75.6 % Description: INTENSITY-INTEGRATION SOFTWARE USED WAS A MODIFIED VERSION OF THE PURDUE OSCILLATION FILM PROCESSING PACKAGE AND DENZO | ||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Jacobo-Molina, A., (1991) Biochemistry, 30, 6351. / pH: 8.8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: FUJI / Detector: IMAGE PLATE / Date: 1992 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Redundancy: 4.3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.13 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 76187 / % possible obs: 86.6 % / Observed criterion σ(I): 2 |
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Processing
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Refinement | Resolution: 2.8→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 125 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.271 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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