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- PDB-2be2: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -

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Entry
Database: PDB / ID: 2be2
TitleCrystal structure of HIV-1 reverse transcriptase (RT) in complex with R221239
Components(REVERSE TRANSCRIPTASE ...) x 2
KeywordsTRANSFERASE / AIDS / HIV / DRUG DESIGN / REVERSE TRANSCRIPTASE / RT / PROTEIN-INHIBITOR COMPLEX / DRUG RESISTANCE
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 / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Retrovirus capsid, C-terminal / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
sucrose / : / Chem-R22 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHimmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. ...Himmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. / Meyer, C. / Andries, K. / Nguyen, C.H. / Grierson, D.S. / Arnold, E.
Citation
Journal: J.Med.Chem. / Year: 2005
Title: Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-Nucleoside Inhibitors Effective against a Broad Range of Drug-Resistant Strains.
Authors: Himmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. / Meyer, C. / Andries, K. / Nguyen, C.H. / Grierson, D.S. / Arnold, E.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: 3-iodo-4-phenoxypyridinones (IOPY's), a New Family of Highly Potent Non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase
Authors: Benjahad, A. / Guillemont, J. / Andries, K. / Nguyen, C.H. / Grierson, D.S.
#2: Journal: J.Med.Chem. / Year: 2005
Title: 4-Benzyl and 4-Benzoyl-3-Dimethylaminopyridin-2(1H)-Ones: In Vitro Evaluation of New C-3-Amino-Substituted and C-5,6-Alkyl-Substituted Analogues Against Clinically Important HIV Mutant Strains
Authors: Benjahad, A. / Croisy, M. / Monneret, C. / Bisagni, E. / Mabire, D. / Coupa, S. / Poncelet, A. / Csoka, I. / Guillemont, J. / Meyer, C. / Andries, K. / Pauwels, R. / De Bethune, M.P. / ...Authors: Benjahad, A. / Croisy, M. / Monneret, C. / Bisagni, E. / Mabire, D. / Coupa, S. / Poncelet, A. / Csoka, I. / Guillemont, J. / Meyer, C. / Andries, K. / Pauwels, R. / De Bethune, M.P. / Himmel, D.M. / Das, K. / Arnold, E. / Nguyen, C.H. / Grierson, D.S.
#3: Journal: J.Med.Chem. / Year: 2004
Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent ...Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent and Effective Against Wild-Type and Drug-Resistant HIV-1 Variants
Authors: Das, K. / Clark Jr., A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M.H. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. ...Authors: Das, K. / Clark Jr., A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M.H. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / De Bethune, M.-P. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A.J. / Arnold, E.
#4: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structures of 8-Cl and 9-Cl TIBO Complexed with Wild-Type HIV-1 RT and 8-Cl TIBO Complexed with the Tyr181Cys HIV-1 RT Drug-Resistant Mutant.
Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#5: Journal: J.Mol.Biol. / Year: 1998
Title: Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution.
Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E.
#6: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors.
Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A.J. / Hughes, S.H. / Arnold, E.
History
DepositionOct 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 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: REVERSE TRANSCRIPTASE P66 SUBUNIT
B: REVERSE TRANSCRIPTASE P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1888
Polymers114,7832
Non-polymers1,4056
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-23 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.853, 68.798, 104.430
Angle α, β, γ (deg.)90.00, 107.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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REVERSE TRANSCRIPTASE ... , 2 types, 2 molecules AB

#1: Protein REVERSE TRANSCRIPTASE P66 SUBUNIT / HIV-1 RT


Mass: 64500.965 Da / Num. of mol.: 1 / Fragment: residues 599-1158 / Mutation: C447S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: isolate BH10 / Description: HIV-1 CLONE 12 / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein REVERSE TRANSCRIPTASE P51 SUBUNIT / HIV-1 RT


Mass: 50281.762 Da / Num. of mol.: 1 / Fragment: residues 599-1028 / Mutation: C447S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: isolate BH10 / Description: HIV-1 CLONE 12 / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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Sugars , 1 types, 2 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 158 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-R22 / 4-(3,5-DIMETHYLPHENOXY)-5-(FURAN-2-YLMETHYLSULFANYLMETHYL)-3-IODO-6-METHYLPYRIDIN-2(1H)-ONE


Mass: 481.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20INO3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.3 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 50mM bisTris Propane, 100mM Ammonium Sulfate, 12% PEG 8000, 10% Glycerol, pH 6.8, temperature 277K, VAPOR DIFFUSION, HANGING DROP, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95043
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95043 Å / Relative weight: 1
ReflectionResolution: 2.4→23 Å / Num. obs: 54672 / % possible obs: 91.7 % / Observed criterion σ(I): -1 / Redundancy: 2.8 % / Biso Wilson estimate: 55.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.9 % / Rsym value: 0.517 / % possible all: 54.9

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Phasing

Phasing dm shellResolution: 2.43→23 Å / Delta phi final: 0.111 / FOM : 0.112 / Reflection: 50774

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S6P

1s6p


Resolution: 2.43→22.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 426382.844 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2483 4.9 %RANDOM
Rwork0.235 ---
obs0.235 50774 88.4 %-
all-57447 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.36 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å25.48 Å2
2--1.3 Å20 Å2
3----5.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.43→22.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 85 154 8262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.11
X-RAY DIFFRACTIONc_mcangle_it7.72
X-RAY DIFFRACTIONc_scbond_it6.79
X-RAY DIFFRACTIONc_scangle_it9.2
LS refinement shellResolution: 2.43→2.58 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 348 5 %
Rwork0.408 6580 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.TOPPROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.TOPION.PARAM
X-RAY DIFFRACTION3WATER.TOPWATER.PARAM
X-RAY DIFFRACTION4221.TOP221.PAR
X-RAY DIFFRACTION5SUC.TOPSUC.PAR

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