[English] 日本語
Yorodumi- PDB-1hmv: THE STRUCTURE OF UNLIGANDED REVERSE TRANSCRIPTASE FROM THE HUMAN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hmv | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF UNLIGANDED REVERSE TRANSCRIPTASE FROM THE HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Components |
| ||||||
Keywords | NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | ||||||
Authors | Rodgers, D.W. / Gamblin, S.J. / Harris, B.A. / Ray, S. / Culp, J.S. / Hellmig, B. / Woolf, D.J. / Debouck, C. / Harrison, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1. Authors: Rodgers, D.W. / Gamblin, S.J. / Harris, B.A. / Ray, S. / Culp, J.S. / Hellmig, B. / Woolf, D.J. / Debouck, C. / Harrison, S.C. #1: Journal: Arch.Biochem.Biophys. / Year: 1989 Title: Recombinant HIV-1 Reverse Transcriptase: Purification, Primary Structure, and Polymerase(Slash)Ribonuclease H Activities Authors: Misrahi, V. / Lazarus, G.M. / Miles, L.M. / Meyers, C.A. / Debouck, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1hmv.cif.gz | 730.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1hmv.ent.gz | 600.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/1hmv ftp://data.pdbj.org/pub/pdb/validation_reports/hm/1hmv | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
3 |
| ||||||||||||||||
4 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||
Details | THE HIV-1 REVERSE TRANSCRIPTASE CONSISTS OF TWO SUBUNITS, P66 (DESIGNATED CHAIN A) AND P51 (DESIGNATED CHAIN B). IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES PER ASYMMETRIC UNIT. COORDINATES FOR ONE MOLECULE ARE CONTAINED IN THIS ENTRY, AND THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW ARE BASED ON THE BEST SUPERPOSITION OF THIS MOLECULE ON EACH OF THE REMAINING THREE. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD COORDINATES FOR THE OTHER THREE MOLECULES PRESENT IN THE ASYMMETRIC UNIT. APPLIED TO WILL GENERATE MTRIX RESIDUES RESIDUES M1 A 1 .. A 554 C 1 .. C 554 M1 B 5 .. B 427 D 5 .. D 427 M2 A 1 .. A 554 E 1 .. E 554 M2 B 5 .. B 427 F 5 .. F 427 M3 A 1 .. A 554 G 1 .. G 554 M3 B 5 .. B 427 H 5 .. H 427 |
-Components
#1: Protein | Mass: 64517.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 POL / Plasmid: POTSKF33 GENE: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase #2: Protein | Mass: 51371.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 POL / Plasmid: POTSKF33 GENE: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase #3: Chemical | ChemComp-MG / Compound details | THE SECONDARY STRUCTURAL | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 4.73 Å3/Da / Density % sol: 73.99 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS Density % sol: 74 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 120337 / % possible obs: 85 % |
Reflection | *PLUS Highest resolution: 3.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.133 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.2→6 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|