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- PDB-6kdo: HIV-1 reverse transcriptase with Q151M/Y115F/F116Y/M184V/F160M:DN... -

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Basic information

Entry
Database: PDB / ID: 6kdo
TitleHIV-1 reverse transcriptase with Q151M/Y115F/F116Y/M184V/F160M:DNA:lamivudine 5'-triphosphate ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 reverse transcriptase p66 subunit
KeywordsTRANSFERASE/DNA / Lamivudine 5'-TRIPHOSPHATE / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / TRANSFERASE-DNA complex / REPLICATION
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 / Retrovirus capsid, C-terminal / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Lamivudine Triphosphate / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.573 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19fk0310113 Japan
CitationJournal: Sci Rep / Year: 2020
Title: Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: 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: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,87213
Polymers255,2236
Non-polymers1,6497
Water3,459192
1
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6077
Polymers127,6113
Non-polymers9964
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-41 kcal/mol
Surface area47060 Å2
MethodPISA
2
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2656
Polymers127,6113
Non-polymers6533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-40 kcal/mol
Surface area47320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.239, 284.239, 95.948
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 HIV-1 reverse transcriptase p66 subunit


Mass: 63985.348 Da / Num. of mol.: 2 / Mutation: Y214F, F215Y, Q250M, F259M, C261S, M283V, C379S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5, UniProt: P12497*PLUS
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S, C867S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

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DNA chain / Sugars , 2 types, 3 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 11764.525 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 , 3 types, 198 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1RZ / Lamivudine Triphosphate / Lamivudine-5'-triphosphate / 3TC Triphosphate / [[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 469.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14N3O12P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 91600 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rrim(I) all: 0.078 / Net I/σ(I): 14.5
Reflection shellResolution: 2.57→2.62 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4362 / Rrim(I) all: 0.892 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XN0

5xn0


Resolution: 2.573→48.668 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.41
RfactorNum. reflection% reflection
Rfree0.2303 4638 5.06 %
Rwork0.1916 --
obs0.1936 91591 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.573→48.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15668 1501 73 192 17434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517839
X-RAY DIFFRACTIONf_angle_d0.90924530
X-RAY DIFFRACTIONf_dihedral_angle_d25.4516823
X-RAY DIFFRACTIONf_chiral_restr0.0552669
X-RAY DIFFRACTIONf_plane_restr0.0082827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5725-2.60180.36851730.31912737X-RAY DIFFRACTION95
2.6018-2.63240.28411080.27172963X-RAY DIFFRACTION100
2.6324-2.66450.29371820.26692886X-RAY DIFFRACTION100
2.6645-2.69820.28341420.25582911X-RAY DIFFRACTION100
2.6982-2.73370.34231350.25992910X-RAY DIFFRACTION100
2.7337-2.77110.27371460.252896X-RAY DIFFRACTION100
2.7711-2.81070.28281680.24322918X-RAY DIFFRACTION100
2.8107-2.85270.31391420.23992887X-RAY DIFFRACTION100
2.8527-2.89730.26831720.24052909X-RAY DIFFRACTION100
2.8973-2.94470.31261750.2392881X-RAY DIFFRACTION100
2.9447-2.99550.2781750.24582899X-RAY DIFFRACTION100
2.9955-3.050.29871750.23772841X-RAY DIFFRACTION100
3.05-3.10860.31061230.23352945X-RAY DIFFRACTION100
3.1086-3.17210.27781670.21052888X-RAY DIFFRACTION100
3.1721-3.2410.28681620.20832890X-RAY DIFFRACTION100
3.241-3.31640.23221470.19932939X-RAY DIFFRACTION100
3.3164-3.39930.25851510.19362892X-RAY DIFFRACTION100
3.3993-3.49120.2281570.19582895X-RAY DIFFRACTION100
3.4912-3.59390.27051540.19472934X-RAY DIFFRACTION100
3.5939-3.70990.24311510.19842893X-RAY DIFFRACTION100
3.7099-3.84240.21891560.1842898X-RAY DIFFRACTION100
3.8424-3.99620.22241820.17322888X-RAY DIFFRACTION100
3.9962-4.1780.18881520.16752916X-RAY DIFFRACTION100
4.178-4.39810.20361460.16712918X-RAY DIFFRACTION100
4.3981-4.67350.18211570.16442863X-RAY DIFFRACTION100
4.6735-5.0340.19311510.16522899X-RAY DIFFRACTION100
5.034-5.53990.21661580.17192912X-RAY DIFFRACTION100
5.5399-6.34010.21871350.20122924X-RAY DIFFRACTION100
6.3401-7.98210.20361740.17972897X-RAY DIFFRACTION100
7.9821-48.67710.17771220.15992924X-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)
11.21250.0226-0.4650.6120.09843.2922-0.0362-0.18380.13120.03490.007-0.09740.14960.19040.01950.26810.00170.03960.3927-0.04240.3916178.1629275.2213-146.3663
23.03850.52940.43151.16410.73552.7265-0.1360.14450.342-0.2225-0.10310.4705-0.3401-0.96080.24620.39810.0821-0.05320.713-0.03420.5703145.9296276.241-155.3164
31.4380.35220.93225.06363.84658.3524-0.0302-0.4733-0.2040.0209-0.10220.22840.5649-0.65790.12440.3739-0.05340.07440.50470.00780.3493174.6947264.3746-147.8952
42.2175-0.0101-0.25751.9617-0.56231.3049-0.0750.23610.1574-0.24150.06070.126-0.0561-0.07830.01390.3203-0.04960.01620.4586-0.02040.3279211.1265281.7379-183.4419
51.1007-0.78730.30723.1456-0.78211.246-0.02120.07820.0238-0.01440.0186-0.21880.01410.33450.010.3265-0.07090.04990.52180.00290.353238.6341262.5131-182.4281
65.01220.5830.30532.5644-0.69113.8290.12250.789-0.4529-0.5938-0.3417-0.12620.57120.30950.22480.5425-0.00810.08730.5922-0.05810.3436207.3502273.9546-191.5031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 2 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 5 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

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