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- PDB-5j2n: HIV-1 reverse transcriptase in complex with DNA that has incorpor... -

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Basic information

Entry
Database: PDB / ID: 5j2n
TitleHIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the P-(post-translocation) site and dTMP at the N-(pre-translocation) site
Components
  • (reverse transcriptase, ...) x 2
  • DNA (27-MER)
  • DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3'
Keywordstransferase/dna / HIV-1 / reverse transcriptase / RT / DNA / double stranded DNA / dsDNA / EFdA / 4'-ethynyl-2-fluoro-2'-deoxyadenosine / EFdA-monophosphate / EFdA-MP / inhibitors / NRTI / TDRTI / translocation defective / pre-translocation / N site / 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 / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.896 Å
AuthorsSalie, Z.L. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076119 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI099284 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112417 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103368 United States
University of MissouriMizzou Advantage United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA).
Authors: Salie, Z.L. / Kirby, K.A. / Michailidis, E. / Marchand, B. / Singh, K. / Rohan, L.C. / Kodama, E.N. / Mitsuya, H. / Parniak, M.A. / Sarafianos, S.G.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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: reverse transcriptase, p66 domain
B: reverse transcriptase, p51 domain
P: DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3'
T: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1575
Polymers131,1334
Non-polymers241
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-66 kcal/mol
Surface area47450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.827, 169.885, 102.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Reverse transcriptase, ... , 2 types, 2 molecules AB

#1: Protein reverse transcriptase, p66 domain / / Pr160Gag-Pol


Mass: 64521.895 Da / Num. of mol.: 1 / Mutation: Q258C, 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 / Plasmid: pCDFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein reverse transcriptase, p51 domain / / Pr160Gag-Pol


Mass: 51382.984 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 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3'


Mass: 6820.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: DNA chain DNA (27-MER)


Mass: 8407.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Non-polymers , 2 types, 5 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8% PEG4000, 25mM MES pH 6.0, 5mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→53.62 Å / Num. obs: 32900 / % possible obs: 99 % / Redundancy: 7.2 % / Biso Wilson estimate: 54.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.055 / Rrim(I) all: 0.149 / Net I/σ(I): 13.4 / Num. measured all: 238525 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.88-3.046.20.8832768544520.6690.3760.962293
9.12-53.626.80.039774611460.9990.0160.04241.299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.41 Å53.62 Å
Translation8.41 Å53.62 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.12data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5J2M

5j2m


Resolution: 2.896→53.623 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1601 4.89 %
Rwork0.2116 31133 -
obs0.2131 32734 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.58 Å2 / Biso mean: 57.3747 Å2 / Biso min: 28.07 Å2
Refinement stepCycle: final / Resolution: 2.896→53.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7879 872 1 4 8756
Biso mean--29.2 63.39 -
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029071
X-RAY DIFFRACTIONf_angle_d0.44312476
X-RAY DIFFRACTIONf_chiral_restr0.0391362
X-RAY DIFFRACTIONf_plane_restr0.0031425
X-RAY DIFFRACTIONf_dihedral_angle_d14.7315289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8955-2.9890.37751300.30892698282896
2.989-3.09580.33451350.293728112946100
3.0958-3.21970.31651250.27128472972100
3.2197-3.36620.23561600.253327632923100
3.3662-3.54370.28191360.236528432979100
3.5437-3.76570.27261650.227327882953100
3.7657-4.05630.25531480.208528272975100
4.0563-4.46430.24051620.182528282990100
4.4643-5.10990.19021380.171228492987100
5.1099-6.43620.21031360.195629043040100
6.4362-53.63240.19761660.179329753141100
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)
10.4918-0.78690.34661.8173-0.93830.44060.07040.1158-0.0018-0.3784-0.0489-0.09670.1891-0.00050.00090.4269-0.01550.02860.415-0.03190.328739.273624.337-29.6116
20.6354-0.3915-0.01881.7781-0.49150.3058-0.1052-0.2233-0.10110.41340.19580.3175-0.1583-0.15860.00020.44730.05640.06690.57430.04670.488718.912639.0468-7.9444
30.43630.07280.13440.9301-0.82970.65020.430.3906-0.0003-0.2277-0.39950.42780.0965-0.1698-0.00180.81970.0456-0.12310.6507-0.00540.581425.187226.4311-35.9083
40.5463-0.90630.41241.179-0.66760.22630.04760.1941-0.71140.217-0.04331.21870.176-0.08070.00170.73840.08470.03930.63570.01080.625128.648325.0047-35.2612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA1 - 558
2X-RAY DIFFRACTION2Chain BB4 - 430
3X-RAY DIFFRACTION3Chain TT703 - 725
4X-RAY DIFFRACTION4Chain PP805 - 823

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