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

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Basic information

Entry
Database: PDB / ID: 6ika
TitleHIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:entecavir-triphosphate ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 RT p66 subunit
KeywordsTRANSFERASE/DNA / ENTECAVIR 5'-TRIPHOSPHATE / 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
Chem-ET9 / 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: 2.598 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 RT p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 RT p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,59414
Polymers255,1436
Non-polymers1,4518
Water2,684149
1
A: HIV-1 RT p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2977
Polymers127,5713
Non-polymers7264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-43 kcal/mol
Surface area47070 Å2
MethodPISA
2
C: HIV-1 RT p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2977
Polymers127,5713
Non-polymers7264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-42 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.405, 285.405, 96.346
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 RT 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 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / References: UniProt: D3XFN7
#2: Protein HIV-1 RT 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 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / 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, 157 molecules

#4: 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
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 58.44 %
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: 2.598→50 Å / Num. obs: 89785 / % possible obs: 99.6 % / Redundancy: 5.42 % / CC1/2: 0.998 / Rrim(I) all: 0.091 / Net I/σ(I): 15.89
Reflection shellResolution: 2.598→2.76 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 14209 / CC1/2: 0.711 / Rrim(I) all: 0.844 / % possible all: 97.4

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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: 2.598→48.869 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.232 4538 5.05 %
Rwork0.1858 --
obs0.1881 89774 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→48.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15682 1495 90 149 17416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01317863
X-RAY DIFFRACTIONf_angle_d1.12124572
X-RAY DIFFRACTIONf_dihedral_angle_d24.8816813
X-RAY DIFFRACTIONf_chiral_restr0.122669
X-RAY DIFFRACTIONf_plane_restr0.0072827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5982-2.62780.35641300.30842476X-RAY DIFFRACTION88
2.6278-2.65870.31471470.28212863X-RAY DIFFRACTION100
2.6587-2.69110.35631470.27422866X-RAY DIFFRACTION100
2.6911-2.72510.31091300.27072867X-RAY DIFFRACTION100
2.7251-2.7610.29951580.25772877X-RAY DIFFRACTION100
2.761-2.79880.2921440.24852870X-RAY DIFFRACTION100
2.7988-2.83880.27151480.2362866X-RAY DIFFRACTION100
2.8388-2.88120.26681760.23242753X-RAY DIFFRACTION100
2.8812-2.92620.32031620.22482880X-RAY DIFFRACTION100
2.9262-2.97420.25111610.21892832X-RAY DIFFRACTION100
2.9742-3.02540.27281740.2222833X-RAY DIFFRACTION100
3.0254-3.08040.30521600.21662857X-RAY DIFFRACTION100
3.0804-3.13970.2831230.21132882X-RAY DIFFRACTION100
3.1397-3.20380.27771730.20222847X-RAY DIFFRACTION100
3.2038-3.27340.27091570.21022860X-RAY DIFFRACTION100
3.2734-3.34950.23921300.20422864X-RAY DIFFRACTION100
3.3495-3.43330.25681620.19192847X-RAY DIFFRACTION100
3.4333-3.52610.21431520.18762842X-RAY DIFFRACTION100
3.5261-3.62980.27631640.18252835X-RAY DIFFRACTION100
3.6298-3.74690.22161380.17912883X-RAY DIFFRACTION100
3.7469-3.88080.2141480.16952826X-RAY DIFFRACTION100
3.8808-4.03610.23321810.16592843X-RAY DIFFRACTION100
4.0361-4.21970.2121570.15862845X-RAY DIFFRACTION100
4.2197-4.4420.18011300.16052882X-RAY DIFFRACTION100
4.442-4.72010.19731570.15382830X-RAY DIFFRACTION100
4.7201-5.08420.17211570.14932880X-RAY DIFFRACTION100
5.0842-5.59520.20711500.16332845X-RAY DIFFRACTION100
5.5952-6.40330.21661310.18792874X-RAY DIFFRACTION100
6.4033-8.06160.20691740.17242830X-RAY DIFFRACTION100
8.0616-48.87730.2051170.17512881X-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)
11.07590.0471-0.47170.4051-0.06592.5988-0.0858-0.05980.0864-0.01050.0372-0.09690.09950.07530.00720.20360.00060.03030.2874-0.05050.3775178.9246276.7315-147.2362
22.76970.57280.23130.97010.62571.863-0.21480.27010.2882-0.1776-0.00440.3735-0.2312-0.72610.19320.28430.0567-0.0460.6159-0.00650.5249146.5705277.4643-156.257
31.15790.1427-0.09634.15892.24024.391-0.1069-0.2484-0.3409-0.2083-0.0480.15090.1795-0.41470.17730.2553-0.0440.03120.34440.00620.3207175.4327265.5452-148.8218
41.7432-0.0112-0.1421.4451-0.4661.0006-0.06180.16660.2213-0.20650.06910.1161-0.0393-0.0533-0.01210.2703-0.05850.01850.36740.00680.3431211.9786282.9863-184.2805
50.9905-0.23940.03282.0543-0.81511.1808-0.00810.03710.0243-0.07930.0021-0.090.04430.28530.01490.2388-0.04120.05990.4096-0.00460.3551239.5662263.638-183.1524
64.12071.40940.05432.747-0.45113.31270.14630.5596-0.23-0.15-0.4635-0.24480.41480.18780.30710.35370.02250.06350.4219-0.02220.3356208.1764274.9537-192.2634
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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