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- PDB-6eli: Structure of HIV-1 reverse transcriptase (RT) in complex with ril... -

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Basic information

Entry
Database: PDB / ID: 6eli
TitleStructure of HIV-1 reverse transcriptase (RT) in complex with rilpivirine and an RNase H inhibitor XZ462
Components
  • Gag-Pol polyprotein
  • reverse transcriptase
KeywordsHYDROLASE / P51/P66 / HETERO DIMER / NNRTI / ribonuclease H INHIBITOR / NONNUCLEOSIDE INHIBITOR / AIDS / HIV / R278474 / DIARYLPYRIMIDINE / DAPY / DNA RECOMBINATION / DNA POLYMERASE / ENDONUCLEASE / MULTIFUNCTIONAL / ENZYME / TRANSFERASE / HYDROLASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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-BA5 / Chem-T27 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDas, K. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI027690 United States
CitationJournal: J. Virol. / Year: 2018
Title: Developing and Evaluating Inhibitors against the RNase H Active Site of HIV-1 Reverse Transcriptase.
Authors: Boyer, P.L. / Smith, S.J. / Zhao, X.Z. / Das, K. / Gruber, K. / Arnold, E. / Burke, T.R. / Hughes, S.H.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: reverse transcriptase
B: Gag-Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0499
Polymers114,1452
Non-polymers9047
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-70 kcal/mol
Surface area47050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.120, 72.920, 109.250
Angle α, β, γ (deg.)90.00, 101.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein reverse transcriptase / Pr160Gag-Pol


Mass: 64105.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Plasmid: PRT52A / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#2: Protein Gag-Pol polyprotein / Pr160Gag-Pol


Mass: 50039.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Plasmid: PRT52A / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

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Non-polymers , 6 types, 378 molecules

#3: Chemical ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine


Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N6 / Comment: medication, inhibitor*YM
#4: Chemical ChemComp-BA5 / methyl 4-azanyl-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxylate / XZ462


Mass: 235.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: PEG 8000, AMMONIUM SULFATE, MGCL2, IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→70.71 Å / Num. obs: 63950 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 45.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.032 / Rrim(I) all: 0.074 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4480 / CC1/2: 0.623 / Rpim(I) all: 0.429 / Rrim(I) all: 0.99 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.2→53.555 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 23.15
RfactorNum. reflection% reflection
Rfree0.2205 1932 3.02 %
Rwork0.1837 --
obs0.1848 63981 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→53.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7955 0 61 371 8387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058265
X-RAY DIFFRACTIONf_angle_d0.84211225
X-RAY DIFFRACTIONf_dihedral_angle_d11.7724966
X-RAY DIFFRACTIONf_chiral_restr0.0521209
X-RAY DIFFRACTIONf_plane_restr0.0061411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.33821090.25154426X-RAY DIFFRACTION100
2.255-2.3160.26341320.23094398X-RAY DIFFRACTION100
2.316-2.38420.25761410.22134395X-RAY DIFFRACTION100
2.3842-2.46110.27331470.2164446X-RAY DIFFRACTION100
2.4611-2.54910.26351300.20884413X-RAY DIFFRACTION100
2.5491-2.65110.23421450.20224375X-RAY DIFFRACTION100
2.6511-2.77180.24321250.19524440X-RAY DIFFRACTION100
2.7718-2.91790.25661470.19344434X-RAY DIFFRACTION100
2.9179-3.10070.26111310.20044420X-RAY DIFFRACTION100
3.1007-3.34010.20941440.19764448X-RAY DIFFRACTION100
3.3401-3.67610.21511580.1834414X-RAY DIFFRACTION100
3.6761-4.20790.20931390.15814448X-RAY DIFFRACTION100
4.2079-5.30080.17021290.1564504X-RAY DIFFRACTION100
5.3008-53.57070.20791550.17634488X-RAY DIFFRACTION98
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)
11.7427-0.2243-0.73821.79180.40272.33810.1898-0.1133-0.11970.5972-0.20550.25420.3343-0.1667-0.01540.7275-0.08870.09040.45210.02450.362142.6755-17.076868.8975
24.04660.7701-0.20871.0826-0.39811.3890.3636-0.5902-0.38260.3668-0.11840.8427-0.2151-0.7405-0.13890.723-0.03910.06810.79640.10370.976921.1679-24.056630.5424
31.9148-0.54281.42732.6222-1.5863.1830.1537-0.1555-0.28860.06990.19030.42720.0544-0.1533-0.28360.29750.0040.0010.242-0.02160.350136.9259-12.980915.479
43.5531-0.21880.02831.71450.01331.4987-0.1007-0.3113-0.5090.09320.0341-0.01160.0977-0.04860.030.15530.0090.03810.32710.05450.285812.88459.2225.8751
53.2548-0.22971.00563.8505-0.31612.6238-0.097-0.04090.22770.3925-0.135-0.1217-0.32680.41240.13620.3728-0.041-0.03890.32330.04460.226855.90651.504636.7975
61.7133-0.20330.80842.3482-0.70961.836-0.19170.01790.60520.7774-0.0905-0.2166-0.60260.47630.09060.7082-0.2056-0.17060.50140.02670.508859.913513.185136.8368
71.37160.06850.59462.2897-0.0273.2686-0.13340.13260.40720.22390.1-0.0361-0.46560.1830.02090.2936-0.04080.02190.29140.03170.328828.312829.37754.5141
82.5549-0.35281.55974.1864-0.54222.0986-0.00860.16760.09880.1949-0.1645-0.0487-0.13080.13370.14090.279-0.0140.03420.2265-0.01760.239742.67512.399717.9492
90.59650.36930.75980.28160.531.01640.2454-0.2937-0.22560.36660.02460.11030.2867-0.1949-0.21390.682-0.0033-0.01330.45260.03560.412950.0402-20.621246.0776
101.14190.043-0.9590.4019-0.83152.40770.1336-0.31110.12320.7285-0.03430.33910.35440.1097-0.05530.9003-0.05990.18620.59690.01390.420444.4588-14.157872.7561
111.62930.30310.98881.10280.23393.02010.3977-0.1707-0.71480.28390.1638-0.16110.65040.0212-0.49180.57010.0224-0.15490.41710.02650.53354.4857-27.956244.1765
121.09510.7788-0.41182.00990.53794.114-0.27330.83830.0713-0.46870.2333-0.78030.23391.3180.14980.7128-0.3121-0.1351.040.25210.921667.358119.743322.5566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 318 )
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 422 )
4X-RAY DIFFRACTION4chain 'A' and (resid 423 through 554 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 83 )
6X-RAY DIFFRACTION6chain 'B' and (resid 84 through 174 )
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 325 )
8X-RAY DIFFRACTION8chain 'B' and (resid 326 through 428 )
9X-RAY DIFFRACTION9chain 'A' and (resid 85 through 121 )
10X-RAY DIFFRACTION10chain 'A' and (resid 122 through 153 )
11X-RAY DIFFRACTION11chain 'A' and (resid 154 through 242 )
12X-RAY DIFFRACTION12chain 'B' and (resid 175 through 239 )

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