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- PDB-6kdm: HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir ... -

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Basic information

Entry
Database: PDB / ID: 6kdm
TitleHIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 reverse transcriptase p66 subunit
KeywordsTRANSFERASE/DNA / Entecavir 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 / 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: 2.32 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 1.1Nov 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.pdbx_ptnr1_label_alt_id / _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 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)256,87416
Polymers255,2396
Non-polymers1,63610
Water8,611478
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)128,4378
Polymers127,6193
Non-polymers8185
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-41 kcal/mol
Surface area46230 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)128,4378
Polymers127,6193
Non-polymers8185
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-39 kcal/mol
Surface area46670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.447, 284.447, 95.773
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: 64033.387 Da / Num. of mol.: 2 / Mutation: Y214F, F215Y, Q250M, 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 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 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): 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, 488 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: 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 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 57.9 %
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 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 125038 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.098 / Net I/σ(I): 11.6
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6180 / Rrim(I) all: 0.944 / % possible all: 100

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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: 5XN1

5xn1


Resolution: 2.32→48.672 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.99
RfactorNum. reflection% reflection
Rfree0.2227 6351 5.08 %
Rwork0.1899 --
obs0.1916 125025 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→48.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15690 1495 102 478 17765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517901
X-RAY DIFFRACTIONf_angle_d0.79424622
X-RAY DIFFRACTIONf_dihedral_angle_d22.9226857
X-RAY DIFFRACTIONf_chiral_restr0.272664
X-RAY DIFFRACTIONf_plane_restr0.0062837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.34640.31132190.27413953X-RAY DIFFRACTION100
2.3464-2.3740.32361980.2693932X-RAY DIFFRACTION100
2.374-2.40290.29511980.26243987X-RAY DIFFRACTION100
2.4029-2.43340.28831850.263992X-RAY DIFFRACTION100
2.4334-2.46540.31662540.25273919X-RAY DIFFRACTION100
2.4654-2.49920.30262340.24753935X-RAY DIFFRACTION100
2.4992-2.53490.30282240.24813947X-RAY DIFFRACTION100
2.5349-2.57270.29411980.243966X-RAY DIFFRACTION100
2.5727-2.61290.29712200.24393955X-RAY DIFFRACTION100
2.6129-2.65570.29321960.24093990X-RAY DIFFRACTION100
2.6557-2.70150.29061990.23483948X-RAY DIFFRACTION100
2.7015-2.75060.26252040.23623964X-RAY DIFFRACTION100
2.7506-2.80350.25972040.23673952X-RAY DIFFRACTION100
2.8035-2.86070.27822180.23313925X-RAY DIFFRACTION100
2.8607-2.92290.27142380.23753962X-RAY DIFFRACTION100
2.9229-2.99090.26442190.22983963X-RAY DIFFRACTION100
2.9909-3.06570.27962380.21793915X-RAY DIFFRACTION100
3.0657-3.14860.25551880.20774006X-RAY DIFFRACTION100
3.1486-3.24120.25572260.19893889X-RAY DIFFRACTION100
3.2412-3.34580.21881940.20014004X-RAY DIFFRACTION100
3.3458-3.46540.22682260.19523946X-RAY DIFFRACTION100
3.4654-3.60410.23712050.18743946X-RAY DIFFRACTION100
3.6041-3.7680.19732080.17553955X-RAY DIFFRACTION100
3.768-3.96660.19432260.16833941X-RAY DIFFRACTION100
3.9666-4.2150.19432210.15653954X-RAY DIFFRACTION100
4.215-4.54020.1682040.15053987X-RAY DIFFRACTION100
4.5402-4.99670.16472020.14473947X-RAY DIFFRACTION100
4.9967-5.71880.17852120.15973962X-RAY DIFFRACTION100
5.7188-7.20130.19062040.17363951X-RAY DIFFRACTION100
7.2013-48.68260.17891890.15913981X-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)
11.12970.0475-0.44410.5572-0.14492.2618-0.10830.0233-0.0037-0.02380.0404-0.08510.1858-0.0270.03840.1965-0.00350.03890.2774-0.04950.3038178.3566275.8128-146.3484
23.01620.65350.21151.08060.4131.5672-0.20010.37150.175-0.17470.04310.3493-0.1215-0.66090.15820.26850.026-0.03210.6308-0.0190.4331146.1482276.6542-155.469
31.71990.27130.21783.86941.89414.2361-0.1782-0.1536-0.3639-0.23140.00590.18260.2375-0.35580.13830.2544-0.04730.0790.3333-0.01590.3024174.813264.6054-147.9997
41.35340.1788-0.18211.2148-0.47330.9957-0.01470.19050.1906-0.18180.04190.076-0.0421-0.0856-0.03120.2396-0.01420.03970.34210.01080.2826211.2337282.0228-183.197
50.7129-0.228-0.04661.7678-0.69511.2110.04870.02430.0343-0.0779-0.0294-0.11020.04150.3065-0.01480.224-0.01860.04430.3898-0.00530.2827238.7465262.8616-181.9422
63.17180.63740.53231.6884-0.40162.78920.2310.4876-0.2402-0.2218-0.4307-0.09370.54780.19690.21310.42160.02960.0810.3953-0.0090.2758207.5116273.9157-191.1011
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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