[English] 日本語
Yorodumi- PDB-4b3p: Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b3p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE/RNA/DNA / HYDROLASE-RNA-DNA COMPLEX / RNASE H / SUBUNIT INTERFACE / HYBRID | |||||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.839 Å | |||||||||
Authors | Lapkouski, M. / Tian, L. / Miller, J.T. / Le Grice, S.F.J. / Yang, W. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation Authors: Lapkouski, M. / Tian, L. / Miller, J.T. / Le Grice, S.F.J. / Yang, W. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4b3p.cif.gz | 223.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4b3p.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b3p ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b3p | HTTPS FTP |
---|
-Related structure data
Related structure data | 4b3oC 4b3qC 1fk9S 1rtdS 4b37 S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 64380.832 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, HIV-1 retropepsin, exoribonuclease H |
---|---|
#2: Protein | Mass: 52973.785 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, HIV-1 retropepsin |
#3: DNA chain | Mass: 8962.752 Da / Num. of mol.: 1 / Fragment: PRIMER DNA / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#4: RNA chain | Mass: 10646.402 Da / Num. of mol.: 1 / Fragment: TEMPLATE RNA / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
Sequence details | P66 MUTATIONS S68G, R83K, I411V, N447S, R461K, Y483H, D498A, V559I P51 MUTATIONS S68G, R83K, I411V, ...P66 MUTATIONS S68G, R83K, I411V, N447S, R461K, Y483H, D498A, V559I P51 MUTATIONS S68G, R83K, I411V, N-TERMINAL MRGSHHHHHH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 62 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: RT COMPLEX WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 50MM SODIUM CACODYLATE PH6.5), 10MM MGCL2, 0.2M KCL, AND 10% PEG4000 (W/V). VAPOR DIFFUSION 4C. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2011 / Details: MIRRORS VERTICAL FOCUSING |
Radiation | Monochromator: DOUBLE CRYSTAL - SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.85→50 Å / Num. obs: 9097 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Biso Wilson estimate: 185.31 Å2 / Rsym value: 0.16 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 4.85→5.02 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.63 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1RTD, 1FK9 Resolution: 4.839→46.096 Å / SU ML: 1.06 / σ(F): 1.34 / Phase error: 50.33 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 185 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.839→46.096 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|