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- PDB-5xn2: HIV-1 reverse transcriptase Q151M:DNA:dGTP ternary complex -

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Basic information

Entry
Database: PDB / ID: 5xn2
TitleHIV-1 reverse transcriptase Q151M:DNA:dGTP ternary complex
Components
  • (Pol protein) x 2
  • 38-MER DNA aptamer
KeywordsTRANSFERASE/DNA / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / entecavir / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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 / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 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: 2.381 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 / 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.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_conn_type.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)257,01315
Polymers255,2396
Non-polymers1,7749
Water5,783321
1
A: Pol protein
B: Pol protein
E: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6778
Polymers127,6193
Non-polymers1,0585
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-47 kcal/mol
Surface area47280 Å2
MethodPISA
2
C: Pol protein
D: Pol protein
F: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3357
Polymers127,6193
Non-polymers7164
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-50 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.694, 285.694, 96.325
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 / HIV-1 reverse transcriptase p51 subunit


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 , 4 types, 329 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 117205 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.063 / Net I/σ(I): 20.6
Reflection shellResolution: 2.38→2.52 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: 2.381→48.903 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2234 5960 5.09 %
Rwork0.1885 --
obs0.1903 117194 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.381→48.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15674 1495 111 321 17601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317885
X-RAY DIFFRACTIONf_angle_d0.59524604
X-RAY DIFFRACTIONf_dihedral_angle_d22.356829
X-RAY DIFFRACTIONf_chiral_restr0.0442670
X-RAY DIFFRACTIONf_plane_restr0.0052831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3809-2.4080.35191860.30623568X-RAY DIFFRACTION95
2.408-2.43630.32351660.28283744X-RAY DIFFRACTION100
2.4363-2.4660.33752300.26923706X-RAY DIFFRACTION100
2.466-2.49720.29382330.26793637X-RAY DIFFRACTION100
2.4972-2.53010.33142190.2533734X-RAY DIFFRACTION100
2.5301-2.56480.3211770.25183674X-RAY DIFFRACTION100
2.5648-2.60140.30042010.24243769X-RAY DIFFRACTION100
2.6014-2.64020.28071780.24223699X-RAY DIFFRACTION100
2.6402-2.68150.28052150.23423740X-RAY DIFFRACTION100
2.6815-2.72540.2911620.24133710X-RAY DIFFRACTION100
2.7254-2.77240.28911970.24473733X-RAY DIFFRACTION100
2.7724-2.82280.27942070.24323728X-RAY DIFFRACTION100
2.8228-2.87710.26622060.24323683X-RAY DIFFRACTION100
2.8771-2.93590.29642160.24643688X-RAY DIFFRACTION100
2.9359-2.99970.26192120.22813746X-RAY DIFFRACTION100
2.9997-3.06950.26532270.22953652X-RAY DIFFRACTION100
3.0695-3.14620.30221670.21433720X-RAY DIFFRACTION100
3.1462-3.23120.24372240.20333690X-RAY DIFFRACTION100
3.2312-3.32630.24691820.20733748X-RAY DIFFRACTION100
3.3263-3.43360.25691900.20143727X-RAY DIFFRACTION100
3.4336-3.55630.23462110.20033685X-RAY DIFFRACTION100
3.5563-3.69870.22951850.18433720X-RAY DIFFRACTION100
3.6987-3.86690.18742000.16763734X-RAY DIFFRACTION100
3.8669-4.07070.20242190.16113655X-RAY DIFFRACTION100
4.0707-4.32560.20191970.15663746X-RAY DIFFRACTION100
4.3256-4.65940.17361950.15223722X-RAY DIFFRACTION100
4.6594-5.12780.16021930.14383693X-RAY DIFFRACTION100
5.1278-5.86870.20072030.16773701X-RAY DIFFRACTION100
5.8687-7.38990.1761850.1723762X-RAY DIFFRACTION100
7.3899-48.91290.17431770.15533720X-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)
10.8946-0.0191-0.34190.43090.06382.1645-0.0822-0.03850.0844-0.00720.0043-0.06960.1367-0.02720.06190.2712-0.00490.03380.346-0.03470.3759179.1122276.7965-147.0209
22.44070.54480.20.97730.43281.5379-0.18830.20230.2783-0.1566-0.02350.3735-0.1485-0.64220.1870.32950.0397-0.04430.666-0.03040.5326146.771277.7814-156.0196
31.65560.22190.14073.52791.6153.799-0.0905-0.1886-0.4132-0.28530.03480.02580.0768-0.44570.04150.3143-0.04180.0570.4019-0.01130.3674175.5871265.7238-148.7163
41.4906-0.0087-0.1490.9368-0.35990.9865-0.00750.1680.1255-0.13670.02050.0943-0.0681-0.0556-0.01690.3092-0.02770.04120.38240.01310.3663212.1511283.217-184.0111
50.6686-0.39550.02271.4694-0.59321.07860.03960.01880.0175-0.0552-0.0072-0.03730.03790.2668-0.02480.359-0.03060.06350.51790.00650.4661239.8692264.0205-182.9355
63.76750.82540.4511.6976-0.37323.31650.31310.4601-0.225-0.0973-0.5176-0.06150.38820.26290.21250.41420.02550.07880.4367-0.00460.3376208.4981275.1691-192.0328
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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