[English] 日本語
Yorodumi
- PDB-3ig1: HIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ig1
TitleHIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol Bound at the RNase H Active Site
Components
  • HIV-1 Reverse Transcriptase p51 subunit
  • HIV-1 Reverse Transcriptase p66 subunit
KeywordsTRANSFERASE / RNASE H INHIBITOR / PROTEIN-INHIBITOR COMPLEX / STRUCTURE-BASED DRUG DESIGN / TROPOLONES / TROPYLIUM ION / DIVALENT CATION CHELATOR / AIDS / DNA-DIRECTED DNA POLYMERASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / RNA-BINDING / RNA-DIRECTED DNA POLYMERASE
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
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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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-JTH / : / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsHimmel, D.M. / Maegley, K.A. / Pauly, T.A. / Arnold, E.
Citation
Journal: Structure / Year: 2009
Title: Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.
Authors: Himmel, D.M. / Maegley, K.A. / Pauly, T.A. / Bauman, J.D. / Das, K. / Dharia, C. / Clark, A.D. / Ryan, K. / Hickey, M.J. / Love, R.A. / Hughes, S.H. / Bergqvist, S. / Arnold, E.
#1: Journal: Nucleic Acids Res. / Year: 2008
Title: Crystal Engineering of HIV-1 Reverse Transcriptase for Structure-based Drug Design
Authors: Bauman, J.D. / Das, K. / Ho, W.C. / Baweja, M. / Himmel, D.M. / Clark Jr., A.D. / Oren, D.A. / Boyer, P.L. / Hughes, S.H. / Shatkin, A.J. / Arnold, E.
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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: HIV-1 Reverse Transcriptase p66 subunit
B: HIV-1 Reverse Transcriptase p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1455
Polymers113,8552
Non-polymers2903
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-35 kcal/mol
Surface area47250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.057, 71.300, 108.541
Angle α, β, γ (deg.)90.000, 105.130, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein HIV-1 Reverse Transcriptase p66 subunit / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / Retropepsin / PR / Reverse transcriptase/ribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 63815.016 Da / Num. of mol.: 1 / Fragment: p66 subunit, residues 600-1154 / Mutation: F759S, C879S
Source method: isolated from a genetically manipulated source
Details: See citation_id 1 above.
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol, POL / Plasmid: pCDF-2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 Reverse Transcriptase p51 subunit


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 subunit, residues 600-1027 / Mutation: C879S
Source method: isolated from a genetically manipulated source
Details: See citation_id 1 above.
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol, POL / Plasmid: pCDF-2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-JTH / 2,7-dihydroxy-4-(propan-2-yl)cyclohepta-2,4,6-trien-1-one / beta-thujaplicinol


Mass: 180.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 50 mM Bicine pH 8.2, 45 mM Ammonium Sulfate, 15 mM Manganese Sulfate, 10 mM Spermine, 5 mM Taurine, 2% PEG 400, 10% PEG 8000 Combined with equal volume of: 10 mM Tris pH 8.0, 75 mM NaCl, 3. ...Details: 50 mM Bicine pH 8.2, 45 mM Ammonium Sulfate, 15 mM Manganese Sulfate, 10 mM Spermine, 5 mM Taurine, 2% PEG 400, 10% PEG 8000 Combined with equal volume of: 10 mM Tris pH 8.0, 75 mM NaCl, 3.5% DMSO, 0.86 mM b-Thujaplicinol, 0.17 mM Reverse Transcriptase, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2007
RadiationMonochromator: Double silicon(111) crystal monochromator and mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. all: 28769 / Num. obs: 28769 / % possible obs: 94.3 % / Observed criterion σ(I): -1.1 / Redundancy: 2.7 % / Biso Wilson estimate: 71.5 Å2 / Rsym value: 0.061 / Χ2: 1.006 / Net I/σ(I): 15.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Num. unique all: 2599 / Rsym value: 0.489 / Χ2: 1.005 / % possible all: 77.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLO

1dlo


Resolution: 2.8→33.75 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.791 / Data cutoff high absF: 199160 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 784 2.8 %RANDOM
Rwork0.238 ---
all0.241 30078 --
obs0.238 27627 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 181.49 Å2 / Biso mean: 89.018 Å2 / Biso min: 26.04 Å2
Baniso -1Baniso -2Baniso -3
1--13.53 Å20 Å26.1 Å2
2---6.74 Å20 Å2
3---20.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.8→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 15 74 7964
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it3.41.5
X-RAY DIFFRACTIONc_mcangle_it5.872
X-RAY DIFFRACTIONc_scbond_it5.382
X-RAY DIFFRACTIONc_scangle_it8.362.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 88 2.3 %
Rwork0.376 3689 -
all-3777 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4allprosth2.parcarbohydrate.top
X-RAY DIFFRACTION5allprosth2.top

+
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