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- PDB-6or7: Structure of HIV-1 Reverse Transcriptase (RT) in complex with DNA... -

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Basic information

Entry
Database: PDB / ID: 6or7
TitleStructure of HIV-1 Reverse Transcriptase (RT) in complex with DNA AND (-)FTC-TP
Components
  • DNA Primer 20-mer
  • DNA template 27-mer
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/DNA / Reverse Transcriptase / ternary complex / (-)FTC-TP / chain terminator / emtricitabine / stereochemistry / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein 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-1RY / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsBertoletti, N. / Chan, A.H. / Anderson, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049551 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active ...Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine.
Authors: Bertoletti, N. / Chan, A.H. / Schinazi, R.F. / Yin, Y.W. / Anderson, K.S.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: p51 RT
P: DNA Primer 20-mer
T: DNA template 27-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,09410
Polymers132,2704
Non-polymers8246
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-106 kcal/mol
Surface area43960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.499, 169.825, 103.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Reverse transcriptase/ribonuclease H


Mass: 64653.090 Da / Num. of mol.: 1 / Mutation: C280S, Q258C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT


Mass: 52748.418 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P04585

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA Primer 20-mer


Mass: 6460.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA template 27-mer


Mass: 8408.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 54 molecules

#5: Chemical ChemComp-1RY / [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 487.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13FN3O12P3S
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.55 % / Description: thin plate
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6-10% (w/v) PEG 8000, 15 mM magnesium sulfate, and 50 mM MES adjusted at pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 48991 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rsym value: 0.093 / Net I/σ(I): 16.64
Reflection shellResolution: 2.53→2.68 Å / Redundancy: 6.98 % / Mean I/σ(I) obs: 1.93 / Num. unique obs: 7702 / CC1/2: 0.778 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KJV

3kjv


Resolution: 2.53→47.572 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2447 5 %
Rwork0.2119 --
obs0.2138 48969 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→47.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7309 843 45 48 8245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038495
X-RAY DIFFRACTIONf_angle_d0.56911784
X-RAY DIFFRACTIONf_dihedral_angle_d16.2734877
X-RAY DIFFRACTIONf_chiral_restr0.0421316
X-RAY DIFFRACTIONf_plane_restr0.0041352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5302-2.58190.37981370.32452611X-RAY DIFFRACTION96
2.5819-2.6380.35731410.31562673X-RAY DIFFRACTION100
2.638-2.69940.37931420.31472709X-RAY DIFFRACTION100
2.6994-2.76690.36151440.35332739X-RAY DIFFRACTION100
2.7669-2.84170.37611420.30442701X-RAY DIFFRACTION100
2.8417-2.92530.33921430.27022721X-RAY DIFFRACTION100
2.9253-3.01970.27891430.26172726X-RAY DIFFRACTION100
3.0197-3.12760.30561440.27052727X-RAY DIFFRACTION100
3.1276-3.25280.27871430.24952717X-RAY DIFFRACTION100
3.2528-3.40080.26231440.24362736X-RAY DIFFRACTION100
3.4008-3.580.29831430.22322721X-RAY DIFFRACTION100
3.58-3.80430.27321440.2052740X-RAY DIFFRACTION100
3.8043-4.09780.22181460.18132762X-RAY DIFFRACTION100
4.0978-4.50990.20321450.16562761X-RAY DIFFRACTION100
4.5099-5.16190.22191460.15852781X-RAY DIFFRACTION100
5.1619-6.50080.19221470.19362792X-RAY DIFFRACTION100
6.5008-47.58010.19271530.17862905X-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)
12.1447-0.6156-0.45125.14710.19583.97260.12340.4986-0.6312-1.0171-0.0130.5140.9225-0.2394-0.09040.8165-0.1191-0.14550.5788-0.12760.731531.4145-9.5467-28.5517
29.7997-5.2807-0.40336.1714-0.80627.172-0.59971.52020.7102-1.37220.0904-0.44860.11240.14520.49471.0626-0.1105-0.07120.5542-0.05890.636639.645-2.3898-33.7113
33.71120.78470.8433.2691-0.25190.1323-0.05680.1851-0.5042-0.24980.16340.3190.1258-0.0642-0.09650.4298-0.0464-0.02430.4255-0.02620.425238.19145.6522-19.2764
46.9982-0.8382-2.25032.2433-0.69594.5074-0.73671.25390.3277-0.2762-0.08720.96491.1946-0.86020.78871.0126-0.1083-0.36890.5462-0.13590.806328.7257-11.6434-30.9475
50.6566-0.1272-0.16013.4094-0.62541.1728-0.00240.0945-0.0922-0.51110.0365-0.18710.2770.0102-0.04740.40120.00140.01690.3227-0.02950.363548.55558.7945-20.6823
61.4606-0.14340.00514.5955-0.56790.53440.05050.29930.1897-0.8729-0.0682-0.3721-0.0869-0.0167-0.01070.49-0.00050.06660.3890.06040.385947.405532.0238-30.5591
72.0085-2.01811.64822.2642-1.45121.9812-0.1751-0.13520.16290.2524-0.0009-0.3654-0.0647-0.07010.19610.3808-0.06950.06040.38470.03330.543637.534853.0821-28.3698
82.6539-0.2326-0.07473.22380.24612.34590.05130.1556-0.0192-0.0193-0.0537-0.03560.1487-0.08-0.00170.3532-0.00540.07790.32020.05990.380324.347857.8198-43.7005
95.6713-0.3804-0.44275.85712.57751.17990.2480.5215-0.3785-0.0944-0.30731.66970.0403-0.7920.10550.5407-0.05180.04090.8150.03261.39158.508315.9268-10.0375
103.4187-1.67590.80895.7920.65252.8011-0.2361-0.0662-0.21750.58830.29560.32070.00520.1418-0.03760.36460.03110.09550.43840.05560.410728.837521.1611-6.7287
112.60360.35690.35872.87630.30610.0707-0.27370.46460.2591-0.260.0209-0.403-0.1344-0.40860.13160.04610.0102-0.010.77690.14861.087710.506821.4375-12.1178
122.0361-2.1743-1.42662.83590.46891.1299-0.0619-0.3495-0.32370.68430.16510.5942-0.2647-0.2231-0.03480.6130.05710.12820.59920.12880.57821.942222.0893-2.4827
133.36990.37471.62974.4571.43512.9634-0.1241-0.7699-0.31280.684-0.28320.2518-0.34690.38240.43820.9241-0.01060.27310.7790.11670.593112.179234.303210.0419
148.6908-0.26191.1741.36872.03543.54290.3234-0.56280.7460.62110.0981-0.4684-2.11140.7334-0.47981.20690.02510.25840.95810.08020.431117.407740.62559.5016
152.68262.1027-1.93357.1655-2.55692.62570.2544-0.30710.25290.359-0.08170.7097-0.212-0.2705-0.19590.3430.00450.0450.5482-0.01030.450110.489765.2159-23.4355
167.592-0.77690.86695.75-0.932.2373-0.07380.30770.11750.36090.2111-0.1418-0.30190.0772-0.11240.36950.01760.07550.4078-0.01440.307521.851244.4132-13.8307
172.4779-0.28021.58664.7253-0.77431.9083-0.66831.4198-0.1727-0.0370.03021.68920.7174-1.17380.74520.5476-0.09460.07330.6392-0.18721.19669.178140.1696-41.8802
181.4056-3.0362.1566.9135-4.64723.2431-0.404-0.2839-0.28680.84170.53380.5913-0.3262-0.198-0.07950.79510.1855-0.04660.62750.06580.691623.082537.8571-35.386
199.45983.9545-0.40955.2161-3.57653.27750.39230.2368-1.76210.205-0.3511-1.13392.2196-0.1664-0.05521.10240.1621-0.05440.5740.03970.951826.906422.0978-33.4568
202.6858-0.8915-1.41467.8213-3.78753.2450.7685-0.1063-0.6635-0.92560.12330.8021-0.2743-0.8407-0.74980.65820.1642-0.0110.55620.07350.471143.415214.5094-34.1123
219.42112.24972.60887.67796.64086.72410.60060.5457-0.4354-2.471-0.5489-0.9819-0.5689-1.093-0.05690.8489-0.0599-0.04960.42290.14290.670535.49474.9066-33.7402
224.41760.9915-2.24813.6687-3.36399.3071-0.3802-0.15390.5205-0.9074-0.15190.9420.9838-0.47480.4390.6745-0.0054-0.19570.3019-0.00740.416238.009219.5024-28.5128
238.5004-6.2991.01076.99071.64392.6650.17830.6513-1.10970.6545-0.5611.75460.7046-0.24070.15510.84970.07290.05310.59490.21260.813621.437432.2609-36.2696
243.6047-3.91543.86196.5787-4.82374.3066-1.22231.0553-0.27820.60460.6474-0.6928-0.9724-0.29830.85120.64680.14230.01291.06630.01441.07375.78249.8211-42.4606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:62 )A1 - 62
2X-RAY DIFFRACTION2( CHAIN A AND RESID 63:79 )A63 - 79
3X-RAY DIFFRACTION3( CHAIN A AND RESID 80:125 )A80 - 125
4X-RAY DIFFRACTION4( CHAIN A AND RESID 126:142 )A126 - 142
5X-RAY DIFFRACTION5( CHAIN A AND RESID 143:277 )A143 - 277
6X-RAY DIFFRACTION6( CHAIN A AND RESID 278:387 )A278 - 387
7X-RAY DIFFRACTION7( CHAIN A AND RESID 388:448 )A388 - 448
8X-RAY DIFFRACTION8( CHAIN A AND RESID 449:553 )A449 - 553
9X-RAY DIFFRACTION9( CHAIN B AND RESID 7:16 )B7 - 16
10X-RAY DIFFRACTION10( CHAIN B AND RESID 17:82 )B17 - 82
11X-RAY DIFFRACTION11( CHAIN B AND RESID 83:86 )B83 - 86
12X-RAY DIFFRACTION12( CHAIN B AND RESID 96:153 )B96 - 153
13X-RAY DIFFRACTION13( CHAIN B AND RESID 154:204 )B154 - 204
14X-RAY DIFFRACTION14( CHAIN B AND RESID 205:240 )B205 - 240
15X-RAY DIFFRACTION15( CHAIN B AND RESID 241:324 )B241 - 324
16X-RAY DIFFRACTION16( CHAIN B AND RESID 325:429 )B325 - 429
17X-RAY DIFFRACTION17( CHAIN P AND RESID 805:808 )P805 - 808
18X-RAY DIFFRACTION18( CHAIN P AND RESID 809:812 )P809 - 812
19X-RAY DIFFRACTION19( CHAIN P AND RESID 813:816 )P813 - 816
20X-RAY DIFFRACTION20( CHAIN P AND RESID 818:821 )P818 - 821
21X-RAY DIFFRACTION21( CHAIN T AND RESID 704:707 )T704 - 707
22X-RAY DIFFRACTION22( CHAIN T AND RESID 708:711 )T708 - 711
23X-RAY DIFFRACTION23( CHAIN T AND RESID 712:721 )T712 - 721
24X-RAY DIFFRACTION24( CHAIN T AND RESID 722:725 )T722 - 725

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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