[English] 日本語
Yorodumi
- PDB-1hqu: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hqu
TitleHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
Components(POL POLYPROTEIN) x 2
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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-HBY / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHsiou, Y. / Ding, J. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.
Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Jr., A.D. / Boyer, P.L. / Lewi, P. / Janssen, P.A. / Kleim, J.P. / Rosner, M. / Hughes, S.H. / Arnold, E.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Structures of Tyr188Leu Mutant and Wild-type HIV-1 Reverse Transcriptase Complexed with the Non-nucleoside Inhibitor HBY 097: Inhibitor Flexibility is a Useful Design Feature for Reducing Drug Resistance
Authors: Hsiou, Y. / Das, K. / Ding, J. / Clark Jr., A.D. / Kleim, J.P. / Rosner, M. / Winkler, I. / Riess, G. / Hughes, S.H. / Arnold, E.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POL POLYPROTEIN
B: POL POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0933
Polymers114,7532
Non-polymers3401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-29 kcal/mol
Surface area47190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.9, 68.9, 103.9
Angle α, β, γ (deg.)90, 106.4, 90
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein POL POLYPROTEIN / REVERSE TRANSCRIPTASE


Mass: 64485.887 Da / Num. of mol.: 1 / Fragment: P66 SUBUNIT / Mutation: K103N, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12; / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein POL POLYPROTEIN / REVERSE TRANSCRIPTASE


Mass: 50266.684 Da / Num. of mol.: 1 / Fragment: P51 SUBUNIT / Mutation: K103N, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12 / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-HBY / (S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL-3,4-DIHYDROQUINOXALIN-2(1H)-THIONE / HBY 097


Mass: 340.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N2O3S2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: BIS-TRIS.PROPANE, AMMONIUN SULFATE, GLYCEROL, PEG 8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMNNRTI1drop
25 %(w/v)beta-OG1drop
330 mg/mlprotein1drop
410 mMTris-HCl1drop
575 mM1dropNaCl
650 mMbis-Tris-propane1reservoir
7100 mMammonium sulfate1reservoir
810glycerol1reservoir
9DMSO1drop
109 %(w/v)PEG80001reservoir

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 1997
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 313409 / Num. obs: 37631 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.448 / % possible all: 45.5
Reflection
*PLUS
Num. obs: 35562 / % possible obs: 94.4 % / Num. measured all: 313409
Reflection shell
*PLUS
% possible obs: 52.7 % / Rmerge(I) obs: 0.468

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BQM

1bqm


Resolution: 2.7→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.345 1709 4.3 %RANDOM
Rwork0.249 ---
obs-34254 81.9 %-
Displacement parametersBiso mean: 61.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7799 0 22 0 7821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 4.3 % / Rfactor obs: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.8 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.7
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.399 / Rfactor obs: 0.341

+
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