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- PDB-5i42: Structure of HIV-1 Reverse Transcriptase in complex with a DNA ap... -

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Basic information

Entry
Database: PDB / ID: 5i42
TitleStructure of HIV-1 Reverse Transcriptase in complex with a DNA aptamer, AZTTP, and CA(2+) ion
Components
  • DNA (38-MER)
  • HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
  • HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
KeywordsTRANSFERASE/DNA / RT / DNA aptamer / AZTTP / polymerase / P site complex / 2-O-METHYLCYTIDINE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / 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
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDas, K. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI027690 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.
Authors: Das, K. / Balzarini, J. / Miller, M.T. / Maguire, A.R. / DeStefano, J.J. / Arnold, E.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (38-MER)
F: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,19910
Polymers255,1056
Non-polymers1,0954
Water00
1
A: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1005
Polymers127,5523
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-42 kcal/mol
Surface area47440 Å2
MethodPISA
2
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
F: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1005
Polymers127,5523
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-40 kcal/mol
Surface area47200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.151, 132.192, 139.658
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT / Pr160Gag-Pol


Mass: 63875.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT / Pr160Gag-Pol


Mass: 51928.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#3: DNA chain DNA (38-MER)


Mass: 11748.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-AZT / 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
Nonpolymer detailsCalcium ion coordination was restricted to > 2.5 A per authors' request

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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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 7% PEG 8000, 25 MM BISTRIS-PROPANE PH 6.8, 75 MM BISTRIS-PROPANE PH 7.4, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE
PH range: 6.8 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 46338 / % possible obs: 94.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 105.27 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Rrim(I) all: 0.058 / Χ2: 1.316 / Net I/av σ(I): 25.846 / Net I/σ(I): 11.5 / Num. measured all: 170385
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.3-3.362.50.339164
3.36-3.422.70.321174.6
3.42-3.482.90.283182
3.48-3.553.10.276190
3.55-3.633.20.252192.9
3.63-3.723.60.213197.6
3.72-3.813.40.176198.1
3.81-3.913.40.153198.2
3.91-4.033.80.129198.9
4.03-4.163.90.103199.1
4.16-4.313.90.093198.8
4.31-4.483.70.077199.4
4.48-4.684.20.071199.3
4.68-4.934.10.067199.5
4.93-5.244.10.06199.4
5.24-5.643.80.056199.2
5.64-6.214.10.053199.6
6.21-7.13.90.044199.5
7.1-8.944.20.03199.8
8.94-5040.02199.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G

5d3g


Resolution: 3.3→48.449 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1890 4.08 %
Rwork0.2206 --
obs0.2217 46295 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→48.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15816 1440 64 0 17320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617929
X-RAY DIFFRACTIONf_angle_d0.62824648
X-RAY DIFFRACTIONf_dihedral_angle_d15.59510490
X-RAY DIFFRACTIONf_chiral_restr0.0442684
X-RAY DIFFRACTIONf_plane_restr0.0052850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.38260.4085880.34182244X-RAY DIFFRACTION67
3.3826-3.4740.36771010.30062670X-RAY DIFFRACTION79
3.474-3.57620.32981260.2862999X-RAY DIFFRACTION90
3.5762-3.69160.33481220.27963191X-RAY DIFFRACTION96
3.6916-3.82350.3141550.25783262X-RAY DIFFRACTION98
3.8235-3.97650.27351440.24813270X-RAY DIFFRACTION98
3.9765-4.15740.27411460.2263321X-RAY DIFFRACTION99
4.1574-4.37650.24561340.21833329X-RAY DIFFRACTION99
4.3765-4.65050.24231320.20563322X-RAY DIFFRACTION99
4.6505-5.00920.22331430.20613353X-RAY DIFFRACTION99
5.0092-5.51260.22551440.213340X-RAY DIFFRACTION100
5.5126-6.30890.28381540.22513326X-RAY DIFFRACTION99
6.3089-7.94280.22371460.21733367X-RAY DIFFRACTION100
7.9428-48.45380.19631550.18553411X-RAY DIFFRACTION99

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