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- PDB-5xn1: HIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate tern... -

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Basic information

Entry
Database: PDB / ID: 5xn1
TitleHIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate ternary complex
Components
  • (Pol protein) x 2
  • 38-MER DNA aptamer
KeywordsTRANSFERASE/DNA / ENTECAVIR 5'-TRIPHOSPHATE / 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 / Chem-ET9 / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.446 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.occupancy / _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)257,12516
Polymers255,2396
Non-polymers1,88610
Water4,846269
1
A: Pol protein
B: Pol protein
E: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6878
Polymers127,6193
Non-polymers1,0685
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-40 kcal/mol
Surface area46780 Å2
MethodPISA
2
C: Pol protein
D: Pol protein
F: 38-MER DNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4378
Polymers127,6193
Non-polymers8185
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-40 kcal/mol
Surface area47130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.707, 284.707, 95.793
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: p66 subunit (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: p51 subunit (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 chain / Sugars , 2 types, 3 molecules EF

#3: DNA chain 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, 278 molecules

#5: Chemical ChemComp-ET9 / [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate / Entecavir 5'-triphosphate


Mass: 517.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N5O12P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
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: 2.446→50 Å / Num. obs: 106838 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rpim(I) all: 0.113 / Net I/σ(I): 12
Reflection shellResolution: 2.45→2.59 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: 2.446→47.018 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.3
RfactorNum. reflection% reflection
Rfree0.2274 5440 5.09 %
Rwork0.1883 --
obs0.1903 106830 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.446→47.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15674 1495 119 269 17557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917892
X-RAY DIFFRACTIONf_angle_d0.90124613
X-RAY DIFFRACTIONf_dihedral_angle_d24.3036857
X-RAY DIFFRACTIONf_chiral_restr0.1732672
X-RAY DIFFRACTIONf_plane_restr0.0072831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.446-2.47380.39111900.31173287X-RAY DIFFRACTION97
2.4738-2.50290.35432000.29293396X-RAY DIFFRACTION100
2.5029-2.53340.31261900.27573370X-RAY DIFFRACTION100
2.5334-2.56550.34551700.26943389X-RAY DIFFRACTION100
2.5655-2.59930.32411990.25743367X-RAY DIFFRACTION100
2.5993-2.63490.28961330.23783428X-RAY DIFFRACTION100
2.6349-2.67250.27272150.2313359X-RAY DIFFRACTION100
2.6725-2.71240.26681400.23013416X-RAY DIFFRACTION100
2.7124-2.75480.28351840.23123389X-RAY DIFFRACTION100
2.7548-2.79990.27591800.23133377X-RAY DIFFRACTION100
2.7999-2.84820.25721810.22773377X-RAY DIFFRACTION100
2.8482-2.90.27681890.23893365X-RAY DIFFRACTION100
2.9-2.95580.29232070.23353324X-RAY DIFFRACTION100
2.9558-3.01610.252000.22793382X-RAY DIFFRACTION100
3.0161-3.08160.27911770.2143368X-RAY DIFFRACTION100
3.0816-3.15330.26531730.20113444X-RAY DIFFRACTION100
3.1533-3.23220.27862030.20373354X-RAY DIFFRACTION100
3.2322-3.31950.22371640.19763360X-RAY DIFFRACTION100
3.3195-3.41720.25151780.18843433X-RAY DIFFRACTION100
3.4172-3.52740.22821920.19263372X-RAY DIFFRACTION100
3.5274-3.65350.25911680.19153385X-RAY DIFFRACTION100
3.6535-3.79970.1921750.17593385X-RAY DIFFRACTION100
3.7997-3.97250.20532080.173331X-RAY DIFFRACTION100
3.9725-4.18190.18391830.1593417X-RAY DIFFRACTION100
4.1819-4.44370.18381660.1523368X-RAY DIFFRACTION100
4.4437-4.78650.19151880.15293401X-RAY DIFFRACTION100
4.7865-5.26760.1721760.14653372X-RAY DIFFRACTION100
5.2676-6.02850.20341730.17393404X-RAY DIFFRACTION100
6.0285-7.590.17491780.17313366X-RAY DIFFRACTION100
7.59-47.02630.19171600.15753404X-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)
10.78360.0023-0.22940.40810.0642.1676-0.0566-0.06050.07770.0241-0.0043-0.04690.1239-0.0210.04630.1915-0.00510.02680.2615-0.01730.2795178.5398275.8753-146.3493
22.52740.46670.21880.89040.42971.4595-0.13280.06620.2969-0.1343-0.10270.3531-0.1793-0.71870.15690.24060.0698-0.04150.6068-0.02120.481146.2728276.9451-155.2847
31.38690.3265-0.23.39141.25552.6843-0.1255-0.1131-0.2474-0.15510.04440.10940.2431-0.33270.0610.2406-0.04120.05030.3270.01160.2599174.9419264.8632-148.032
41.58830.0083-0.24291.0601-0.30640.9285-0.05190.14850.1225-0.17060.04080.0715-0.0264-0.04340.00150.2493-0.04890.03030.34040.01430.3114211.4575282.2919-183.193
50.6729-0.4016-0.00211.6335-0.61911.06390.00920.01460.0239-0.10.0078-0.07550.05940.2746-0.01520.2435-0.03470.06190.41920.02240.3615239.0183263.0804-182.2041
63.67930.81060.21481.51990.15742.87790.19710.5175-0.275-0.1026-0.3896-0.12110.40660.14650.19480.3778-0.00160.05160.40630.00330.2877207.833274.2962-191.2264
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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