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- PDB-5xn0: HIV-1 reverse transcriptase Q151M:DNA binary complex -

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Basic information

Entry
Database: PDB / ID: 5xn0
TitleHIV-1 reverse transcriptase Q151M:DNA binary complex
Components
  • (Pol protein) x 2
  • 38-MER DNA aptamer
KeywordsTRANSFERASE/DNA / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / 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 / 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 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
sucrose / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsYasutake, Y. / Tamura, N. / Hayashi, H. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Sci Rep / Year: 2018
Title: HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir.
Authors: Yasutake, Y. / Hattori, S.I. / Hayashi, H. / Matsuda, K. / Tamura, N. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionMay 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
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 / struct_asym / struct_conn / 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.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pol protein
B: Pol protein
E: 38-MER DNA aptamer
C: Pol protein
D: Pol protein
F: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,04212
Polymers255,2396
Non-polymers8036
Water1,72996
1
A: Pol protein
B: Pol protein
E: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2387
Polymers127,6193
Non-polymers6194
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-41 kcal/mol
Surface area47270 Å2
MethodPISA
2
C: Pol protein
D: Pol protein
F: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,8045
Polymers127,6193
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-47 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.091, 284.091, 95.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Pol protein


Mass: 64033.387 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 100-654 / Mutation: Q151M, C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: D3XFN7, UniProt: P12497*PLUS
#2: Protein Pol protein


Mass: 51861.547 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 100-527 / Mutation: C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: D3XFN7, UniProt: P12497*PLUS

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DNA/RNA hybrid / Sugars , 2 types, 3 molecules EF

#3: DNA/RNA hybrid 38-MER DNA aptamer


Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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 , 2 types, 101 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM bis-Tris-HCl pH 6.0, 60 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 1.5-3% PEG 6000, 2-4% sucrose, 4-8% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.596→50 Å / Num. obs: 88842 / % possible obs: 100 % / Redundancy: 5.2 % / Rpim(I) all: 0.084 / Net I/σ(I): 16.9
Reflection shellResolution: 2.6→2.75 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G

5d3g


Resolution: 2.596→48.605 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2263 4479 5.04 %
Rwork0.1847 --
obs0.1868 88833 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.596→48.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15674 1495 53 96 17318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917818
X-RAY DIFFRACTIONf_angle_d1.14224495
X-RAY DIFFRACTIONf_dihedral_angle_d24.426821
X-RAY DIFFRACTIONf_chiral_restr0.2572663
X-RAY DIFFRACTIONf_plane_restr0.0062827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.596-2.62550.32361110.26652812X-RAY DIFFRACTION99
2.6255-2.65640.30881740.25282847X-RAY DIFFRACTION100
2.6564-2.68880.27271320.24732761X-RAY DIFFRACTION100
2.6888-2.72280.29361300.25282855X-RAY DIFFRACTION100
2.7228-2.75870.30051490.25062784X-RAY DIFFRACTION100
2.7587-2.79650.28771480.24492824X-RAY DIFFRACTION100
2.7965-2.83640.28481560.24392823X-RAY DIFFRACTION100
2.8364-2.87870.29431760.24592799X-RAY DIFFRACTION100
2.8787-2.92370.3051520.25292819X-RAY DIFFRACTION100
2.9237-2.97160.30211640.23912801X-RAY DIFFRACTION100
2.9716-3.02290.27891670.23852754X-RAY DIFFRACTION100
3.0229-3.07780.29831490.21712827X-RAY DIFFRACTION100
3.0778-3.1370.27611350.2042794X-RAY DIFFRACTION100
3.137-3.2010.2561710.1992862X-RAY DIFFRACTION100
3.201-3.27060.26681440.20362785X-RAY DIFFRACTION100
3.2706-3.34670.21841290.19842838X-RAY DIFFRACTION100
3.3467-3.43040.26651670.20072775X-RAY DIFFRACTION100
3.4304-3.52310.23951560.2032820X-RAY DIFFRACTION100
3.5231-3.62670.28641460.19352800X-RAY DIFFRACTION100
3.6267-3.74370.24051400.18612848X-RAY DIFFRACTION100
3.7437-3.87750.19951520.17552808X-RAY DIFFRACTION100
3.8775-4.03270.21431750.1672767X-RAY DIFFRACTION100
4.0327-4.21610.19221570.15782815X-RAY DIFFRACTION100
4.2161-4.43830.17191280.15452833X-RAY DIFFRACTION100
4.4383-4.71610.1781510.15332822X-RAY DIFFRACTION100
4.7161-5.07990.17611530.14622821X-RAY DIFFRACTION100
5.0799-5.59040.20361460.16672802X-RAY DIFFRACTION100
5.5904-6.39780.22361370.18482826X-RAY DIFFRACTION100
6.3978-8.05460.18991700.16872796X-RAY DIFFRACTION100
8.0546-48.61320.19081140.15132836X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89270.0357-0.20160.3613-0.0412.3128-0.0244-0.10510.1450.0469-0.0144-0.0383-0.00250.06270.03680.253-0.02660.03190.3097-0.02520.3593178.2378274.9799-145.8522
22.59750.44440.03620.92320.67642.3859-0.05340.170.3813-0.1017-0.12060.3651-0.2817-0.84420.1560.32170.0988-0.00120.64380.00310.5734145.901276.1185-154.6106
32.090.35080.14223.69311.79993.9238-0.0258-0.2845-0.2381-0.0146-0.00020.22420.3749-0.42890.01630.29-0.05470.04170.35220.03950.2831174.5802264.1894-147.4827
42.0420.1738-0.31391.3118-0.24691.0784-0.14580.220.0491-0.29180.13910.0843-0.02770.00580.01150.3601-0.09910.03040.4581-0.00540.4056210.8448281.6732-183.26
51.2838-0.4685-0.1022.2825-0.49160.9177-0.1575-0.0251-0.1728-0.16530.176-0.2860.13490.2297-0.00910.4229-0.09180.13820.5282-0.01430.5682238.37262.279-182.1926
64.51650.7302-0.07741.87961.40383.110.10870.5529-0.274-0.0926-0.2743-0.00670.2810.08690.12010.4236-0.06530.02470.52030.0110.3181207.3273273.8788-190.9892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 3 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 4 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

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