[English] 日本語
Yorodumi
- PDB-1dtq: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dtq
TitleCRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-1 (PETT131A94)
Components
  • HIV-1 RT A-CHAIN
  • HIV-1 RT B-CHAIN
KeywordsHYDROLASE/TRANSFERASE / HIV-1 reverse transcriptase AIDS / non-nucleoside inhibitor / drug design / HYDROLASE-TRANSFERASE COMPLEX
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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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-FPT / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsRen, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Phenylethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases. Structural and biochemical analyses.
Authors: Ren, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
#1: Journal: J.Med.Chem. / Year: 1999
Title: Crystallographic analysis of the binding modes of thiazoloisoindolinone non-nucleoside inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies.
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Stuart, D.I. / Stammers, D.K.
#2: Journal: J.Med.Chem. / Year: 1999
Title: Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants.
Authors: Hopkins, A.L. / Ren, J. / Tanaka, H. / Baba, M. / Okamato, M. / Stuart, D.I. / Stammers, D.K.
#3: Journal: Biochemistry / Year: 1998
Title: Crystal structures of HIV-1 reverse transcriptase in complex with carboxanilide derivatives.
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Warren, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: 3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes.
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Jones, E.Y. / Kirby, I. / Keeling, J. / Ross, C.K. / Larder, B.A. / Stuart, D.I. / Stammers, D.K.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration.
Authors: Esnouf, R.M. / Ren, J. / Garman, E.F. / Somers, D.O. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this nonnucleoside inhibitor.
Authors: Esnouf, R.M. / Ren, J. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#7: Journal: J.Med.Chem. / Year: 1996
Title: Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors.
Authors: Hopkins, A.L. / Ren, J. / Esnouf, R.M. / Willcox, B.E. / Jones, E.Y. / Ross, C. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I.
#8: Journal: Structure / Year: 1995
Title: The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design.
Authors: Ren, J. / Esnouf, R. / Hopkins, A. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D.
#9: Journal: Nat.Struct.Biol. / Year: 1995
Title: High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
Authors: Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D.
#10: Journal: Nat.Struct.Biol. / Year: 1995
Title: Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors.
Authors: Esnouf, R. / Ren, J. / Ross, C. / Jones, Y. / Stammers, D. / Stuart, D.
#11: Journal: J.Mol.Biol. / Year: 1994
Title: Crystals of HIV-1 reverse transcriptase diffracting to 2.2 A resolution.
Authors: Stammers, D.K. / Somers, D.O. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J.S. / Esnouf, R.M. / Garman, E.F.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Database references / Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 RT A-CHAIN
B: HIV-1 RT B-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3393
Polymers115,9942
Non-polymers3451
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-32 kcal/mol
Surface area45080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.1, 115.0, 65.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HIV-1 RT A-CHAIN


Mass: 64594.949 Da / Num. of mol.: 1 / Fragment: P66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Bacteria (eubacteria) / References: UniProt: P04585
#2: Protein HIV-1 RT B-CHAIN


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: P51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Bacteria (eubacteria) / References: UniProt: P04585
#3: Chemical ChemComp-FPT / N-[[3-FLUORO-4-ETHOXY-PYRID-2-YL]ETHYL]-N'-[5-NITRILOMETHYL-PYRIDYL]-THIOUREA


Mass: 345.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16FN5OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: see reference 11, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Details: Ren, J., (1995) Nat.Struct.Biol., 2, 293.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG34001reservoir
2citrate/phosphate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 25847 / % possible obs: 95.9 % / Observed criterion σ(I): -1.5 / Redundancy: 3.45 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.525 / Num. unique all: 2203 / % possible all: 82.6
Reflection
*PLUS
Num. measured all: 89165
Reflection shell
*PLUS
% possible obs: 82.6 % / Num. unique obs: 2203

-
Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Due to the low ratio between the number of reflections and the number of parameters to be refined, positional restraints were applied to all atoms distant from the NNRTI-binding site ...Details: Due to the low ratio between the number of reflections and the number of parameters to be refined, positional restraints were applied to all atoms distant from the NNRTI-binding site (defined as greater than 25 anstrom from the CA atom of residue 188) throughout the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1205 -random
Rwork0.224 ---
obs0.213 24936 95 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7637 0 24 26 7687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more