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- PDB-6ik9: HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F1... -

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Basic information

Entry
Database: PDB / ID: 6ik9
TitleHIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:dGTP ternary complex
Components
  • (HIV-1 reverse transcriptase ...) x 2
  • DNA/RNA (38-MER)
KeywordsTRANSFERASE/DNA / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / entecavir / 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 / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 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: 2.435 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fk0310113 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified ...Title: Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors.
Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionOct 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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 reverse transcriptase p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 reverse transcriptase p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,57414
Polymers255,1436
Non-polymers1,4318
Water5,423301
1
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 reverse transcriptase p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2877
Polymers127,5713
Non-polymers7164
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12980 Å2
ΔGint-49 kcal/mol
Surface area46320 Å2
MethodPISA
2
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 reverse transcriptase p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2877
Polymers127,5713
Non-polymers7164
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-53 kcal/mol
Surface area47060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.869, 284.869, 95.892
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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HIV-1 reverse transcriptase ... , 2 types, 4 molecules ACBD

#1: Protein HIV-1 reverse transcriptase p66 subunit


Mass: 63985.387 Da / Num. of mol.: 2
Mutation: G211S, D212A, Y214F, F215Y, Q250M, I258L, F259L, C261S, C379S
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
#2: Protein 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 1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P12497

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DNA chain , 1 types, 2 molecules EF

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


Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 309 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 301 / 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: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% 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: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 108564 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rrim(I) all: 0.075 / Net I/σ(I): 18.32
Reflection shellResolution: 2.43→2.58 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 17460 / CC1/2: 0.738 / Rrim(I) all: 0.83 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XN1

5xn1


Resolution: 2.435→48.741 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.8
RfactorNum. reflection% reflection
Rfree0.2252 5558 5.12 %
Rwork0.1865 --
obs0.1884 108555 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.435→48.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15682 1495 88 301 17566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717861
X-RAY DIFFRACTIONf_angle_d0.81824568
X-RAY DIFFRACTIONf_dihedral_angle_d24.5276817
X-RAY DIFFRACTIONf_chiral_restr0.1082669
X-RAY DIFFRACTIONf_plane_restr0.0052827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4347-2.46230.39422220.32813308X-RAY DIFFRACTION97
2.4623-2.49130.36492040.2933384X-RAY DIFFRACTION100
2.4913-2.52170.33742060.27723472X-RAY DIFFRACTION100
2.5217-2.55360.33771610.27023399X-RAY DIFFRACTION100
2.5536-2.58720.32581870.26183455X-RAY DIFFRACTION100
2.5872-2.62260.29981750.25023445X-RAY DIFFRACTION100
2.6226-2.66010.27371830.2333470X-RAY DIFFRACTION100
2.6601-2.69980.27841760.22513443X-RAY DIFFRACTION100
2.6998-2.7420.28911640.2263454X-RAY DIFFRACTION100
2.742-2.78690.24591790.21823413X-RAY DIFFRACTION100
2.7869-2.8350.25791800.21553477X-RAY DIFFRACTION100
2.835-2.88650.28392180.2283403X-RAY DIFFRACTION100
2.8865-2.94210.28081870.22383428X-RAY DIFFRACTION100
2.9421-3.00210.27152090.22993419X-RAY DIFFRACTION100
3.0021-3.06740.27761970.21983417X-RAY DIFFRACTION100
3.0674-3.13870.29381580.20163448X-RAY DIFFRACTION100
3.1387-3.21720.25052050.19323414X-RAY DIFFRACTION100
3.2172-3.30420.23721720.19413481X-RAY DIFFRACTION100
3.3042-3.40140.23731790.18323410X-RAY DIFFRACTION100
3.4014-3.51110.18881810.18353449X-RAY DIFFRACTION100
3.5111-3.63660.25211880.18453411X-RAY DIFFRACTION100
3.6366-3.78210.2141690.183456X-RAY DIFFRACTION100
3.7821-3.95420.19822170.16963437X-RAY DIFFRACTION100
3.9542-4.16250.19671760.15853447X-RAY DIFFRACTION100
4.1625-4.42320.19761760.15883456X-RAY DIFFRACTION100
4.4232-4.76440.19431880.15743422X-RAY DIFFRACTION100
4.7644-5.24340.18491860.15573434X-RAY DIFFRACTION100
5.2434-6.00090.19741710.17923453X-RAY DIFFRACTION100
6.0009-7.5560.19051760.17733427X-RAY DIFFRACTION100
7.556-48.75090.1731680.15933465X-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)
11.10210.0991-0.47460.448-0.15222.4173-0.1085-0.00820.0642-0.01380.0549-0.11230.1450.07410.0360.22180.01090.02390.3035-0.06110.4617178.5715276.1775-146.5442
22.91380.6950.30410.99960.6172.1408-0.23060.34780.2692-0.2039-0.00710.3978-0.1979-0.71590.20220.29560.0463-0.05260.6302-0.01940.614146.3116276.8668-155.5316
30.5951-0.1498-0.48384.15362.09724.709-0.2097-0.1286-0.3247-0.1921-0.02630.24690.4255-0.44540.19150.297-0.03570.04260.3842-0.02170.4406175.0823265.0173-148.1339
41.6302-0.0633-0.10781.2013-0.48841.1658-0.04780.14060.1871-0.15990.05650.1301-0.0692-0.0784-0.02070.2627-0.03670.01510.3524-0.00660.4288211.5723282.4099-183.4213
50.7426-0.45550.09232.0424-0.83171.21420.01870.01360.0547-0.0424-0.0276-0.08680.03570.29570.00760.2438-0.0450.04610.40810.00590.4338239.1206263.1635-182.2661
64.08061.24320.07563.3147-0.33223.76620.09110.6206-0.3047-0.2068-0.3802-0.2480.57520.18120.26560.38590.01770.0710.4422-0.03160.4091207.796274.3673-191.3542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 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 1 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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