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- PDB-1t03: HIV-1 reverse transcriptase crosslinked to tenofovir terminated t... -

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Basic information

Entry
Database: PDB / ID: 1t03
TitleHIV-1 reverse transcriptase crosslinked to tenofovir terminated template-primer (complex P)
Components
  • (POL polyprotein) x 2
  • (Synthetic oligonucleotide ...) x 2
  • (monoclonal antibody ...) x 2
KeywordsTransferase/Antibody/DNA / HIV-1 RT / tenofovir / RT-DNA complex / Transferase-Antibody-DNA COMPLEX
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 / structural molecule activity / host cell plasma membrane / virion membrane / 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 / Immunoglobulins / Roll / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTuske, S. / Sarafianos, S.G. / Ding, J. / Arnold, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir
Authors: Tuske, S. / Sarafianos, S.G. / Clark Jr., A.D. / Ding, J. / Naeger, L.K. / White, K.L. / Miller, M.D. / Gibbs, C.S. / Boyer, P.L. / Clark, P. / Wang, G. / Gaffney, B.L. / Jones, R.A. / ...Authors: Tuske, S. / Sarafianos, S.G. / Clark Jr., A.D. / Ding, J. / Naeger, L.K. / White, K.L. / Miller, M.D. / Gibbs, C.S. / Boyer, P.L. / Clark, P. / Wang, G. / Gaffney, B.L. / Jones, R.A. / Jerina, D.M. / Hughes, S.H. / Arnold, E.
History
DepositionApr 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE The sequence of the FAB heavy and light chains are not available in any of the database ...SEQUENCE The sequence of the FAB heavy and light chains are not available in any of the database sequence. RESIDUE MRG 817 OF THE P CHAIN IS CROSSLINKED TO CHAIN A RESIDUE C258.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Synthetic oligonucleotide template
P: Synthetic oligonucleotide primer
A: POL polyprotein
B: POL polyprotein
L: monoclonal antibody light chain
H: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,5317
Polymers177,5066
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.780, 166.780, 221.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

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Synthetic oligonucleotide ... , 2 types, 2 molecules TP

#1: DNA chain Synthetic oligonucleotide template


Mass: 8367.386 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain Synthetic oligonucleotide primer


Mass: 6430.258 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 2 types, 2 molecules AB

#3: Protein POL polyprotein


Mass: 64249.660 Da / Num. of mol.: 1 / Fragment: Reverse transcriptase, p66 subunit / Mutation: Q258C, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#4: Protein POL polyprotein


Mass: 51095.617 Da / Num. of mol.: 1 / Fragment: Reverse transcriptase, p51 subunit / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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Antibody , 2 types, 2 molecules LH

#5: Antibody monoclonal antibody light chain /


Mass: 23362.650 Da / Num. of mol.: 1 / Fragment: Fab light chain domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Antibody monoclonal antibody heavy chain /


Mass: 24000.814 Da / Num. of mol.: 1 / Fragment: Fab heavy chain domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 4.98 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM cacodylate, 33% ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylateCacodylic acid11
2ammonium sulfate11
3H2O11
4cacodylateCacodylic acid12
5ammonium sulfate12
6H2O12

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2001
RadiationMonochromator: Bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 63979 / % possible obs: 95 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.6
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4741 / % possible all: 74.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N5Y

1n5y


Resolution: 3.1→20 Å / Isotropic thermal model: isotropic / σ(F): 1.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2417 -random
Rwork0.256 ---
all-63680 --
obs-59819 93.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.99 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 908 1 0 12253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.54
LS refinement shellResolution: 3.1→3.12 Å /
RfactorNum. reflection
Rfree0.44 26
Rwork0.41 -

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