[English] 日本語
![](img/lk-miru.gif)
- PDB-1rtd: STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1rtd | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / COMPLEX(NUCLEOTIDYLTRANSFERASE / DNA / DNTP) / PROTEIN/DNA / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / exoribonuclease H activity / protein processing / 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 / peptidase activity / 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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chopra, R. / Huang, H. / Verdine, G.L. / Harrison, S.C. | ||||||
![]() | ![]() Title: Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Authors: Huang, H. / Chopra, R. / Verdine, G.L. / Harrison, S.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 447.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 360.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 540.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 590.3 KB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 66 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||||||||||
Details | THE HIV-1 REVERSE TRANSCRIPTASE CONSISTS OF TWO SUBUNITS, P66 (DESIGNATED BY CHAINS A AND C) AND P51 (DESIGNATED BY CHAINS B AND D). THE DNA DUPLEX IS COMPOSED OF TEMPLATE (DESIGNATED CHAIN E) AND PRIMER (DESIGNATED CHAIN F). THE BOUND DEOXY-THYMINE TRIPHOSPHATE HAS CHAIN IDENTIFIER A. IN THIS CRYSTAL FORM THERE ARE TWO REVERSE TRANSCRIPTASE COMPLEXES PER ASYMMETRIC UNIT. ONE MOLECULE WAS SIGNIFICANTLY BETTER ORDERED THAN THE OTHER. COORDINATES FOR BOTH MOLECULES ARE CONTAINED IN THIS ENTRY, AND THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW WERE THOSE USED TO GENERATE CHAINS C,D,G, AND H FROM A,B,E, AND F DURING THE COURSE OF REFINEMENT. |
-
Components
-DNA chain , 2 types, 4 molecules EGFH
#1: DNA chain | Mass: 8327.361 Da / Num. of mol.: 2 / Mutation: C2-THIOL TETHER AT TEMPLATE GUANINE 11 / Source method: obtained synthetically #2: DNA chain | Mass: 6416.123 Da / Num. of mol.: 2 / Fragment: PRIMER / Mutation: C2-THIOL TETHER AT TEMPLATE GUANINE 11 / Source method: obtained synthetically |
---|
-PROTEIN (REVERSE ... , 2 types, 4 molecules ACBD
#3: Protein | Mass: 63869.148 Da / Num. of mol.: 2 / Fragment: P61 / Mutation: P1K, Q258C, E478Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 51399.047 Da / Num. of mol.: 2 / Fragment: P50 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 2 types, 8 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/TTP.gif)
#5: Chemical | ChemComp-MG / #6: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→18 Å / Num. obs: 54281 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.103 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.372 / % possible all: 84.3 |
Reflection | *PLUS Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 84.3 % / Num. unique obs: 4802 / Rmerge(I) obs: 0.372 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.3 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|