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- PDB-3ig1: HIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol... -

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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 / 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-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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