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- PDB-4b3q: Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Con... -

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Basic information

Entry
Database: PDB / ID: 4b3q
TitleStructures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface
Components
  • P51 RT
  • PRIMER DNA
  • REVERSE TRANSCRIPTASE/RIBONUCLEASE H
  • TEMPLATE RNA
KeywordsHYDROLASE/DNA/RNA / HYDROLASE-DNA-RNA COMPLEX / RNASE H / HYBRID
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / exoribonuclease H activity / protein processing / host multivesicular body / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein binding / membrane
Similarity search - Function
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 ...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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-NVP / DNA / DNA (> 10) / RNA / RNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsLapkouski, M. / Tian, L. / Miller, J.T. / Le Grice, S.F.J. / Yang, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation
Authors: Lapkouski, M. / Tian, L. / Miller, J.T. / Le Grice, S.F.J. / Yang, W.
History
DepositionJul 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE/RIBONUCLEASE H
B: P51 RT
D: PRIMER DNA
R: TEMPLATE RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1145
Polymers135,8484
Non-polymers2661
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-69.4 kcal/mol
Surface area52220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.700, 272.700, 233.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein REVERSE TRANSCRIPTASE/RIBONUCLEASE H / EXORIBONUCLEASE H / P66 RT / REVERSE TRANSCRIPTASE P66 SUBUNIT


Mass: 64423.855 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, HIV-1 retropepsin
#2: Protein P51 RT / REVERSE TRANSCRIPTASE P51 SUBUNIT


Mass: 52973.785 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: P04585
#3: DNA chain PRIMER DNA


Mass: 7670.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain TEMPLATE RNA


Mass: 10779.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-NVP / 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE / NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE


Mass: 266.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O / Comment: medication, antiretroviral*YM
Sequence detailsP66 MUTATIONS S68G, R83K, I411V, N477S, R461K, Y483H, D498N, V559I P51 MUTATIONS S68G, R83K, I411V, ...P66 MUTATIONS S68G, R83K, I411V, N477S, R461K, Y483H, D498N, V559I P51 MUTATIONS S68G, R83K, I411V, N-TERMINAL MRGSHHHHHHGSQL

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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: 6 Å3/Da / Density % sol: 82 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: RT COMPLEX WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 1.8M (NH4)2SO4, 50MM TRIS HCL (PH8.5), AND 25MM MGSO4. VAPOR DIFFUSION 4C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1
DetectorType: MARRESEARCH MAR300 / Detector: CCD / Date: Jul 9, 2011 / Details: ADJUSTABLE FOCUS K-B PAIR SI MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5→60 Å / Num. obs: 14646 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 170.34 Å2 / Rsym value: 0.14 / Net I/σ(I): 14.8
Reflection shellResolution: 5→5.09 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RTD, 1FK9

1rtd

1fk9


Resolution: 5→29.987 Å / SU ML: 1.13 / σ(F): 1 / Phase error: 49.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4073 662 5.1 %
Rwork0.361 --
obs0.3632 13005 89.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149 Å2
Refinement stepCycle: LAST / Resolution: 5→29.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7535 878 20 0 8433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088737
X-RAY DIFFRACTIONf_angle_d0.80212103
X-RAY DIFFRACTIONf_dihedral_angle_d13.783303
X-RAY DIFFRACTIONf_chiral_restr0.0541370
X-RAY DIFFRACTIONf_plane_restr0.0041384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.0003-5.38440.46911280.44272161X-RAY DIFFRACTION80
5.3844-5.92250.41451150.432327X-RAY DIFFRACTION85
5.9225-6.77090.45321520.42222435X-RAY DIFFRACTION90
6.7709-8.49830.3911350.3812648X-RAY DIFFRACTION96
8.4983-29.98710.38151320.3052772X-RAY DIFFRACTION98

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