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- PDB-7lqu: Crystal Structure of HIV-1 RT in Complex with NBD-14075 -

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Basic information

Entry
Database: PDB / ID: 7lqu
TitleCrystal Structure of HIV-1 RT in Complex with NBD-14075
Components
  • Reverse transcriptase p51
  • Reverse transcriptase p66
KeywordsTRANSFERASE/INHIBITOR / Human immunodeficiency virus 1 / non nucleotide-reverse transcriptase inhibitor / TRANSFERASE / TRANSFERASE-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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-YBD / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLosada, N. / Ruiz, F.X. / Gruber, K. / Das, K. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)MERIT Award R37 AI027690 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites.
Authors: Losada, N. / Ruiz, F.X. / Curreli, F. / Gruber, K. / Pilch, A. / Das, K. / Debnath, A.K. / Arnold, E.
History
DepositionFeb 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: 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 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Reverse transcriptase p66
B: Reverse transcriptase p51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7696
Polymers114,0862
Non-polymers6834
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: 1 biological assembly in the asymmetric unit: A,B
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-78 kcal/mol
Surface area47350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.679, 73.050, 107.290
Angle α, β, γ (deg.)90.000, 99.580, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Reverse transcriptase p66


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase p51


Mass: 50096.539 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#3: Chemical ChemComp-YBD / ~{N}-[(1~{R})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-5-(4-chloranyl-3-fluoranyl-phenyl)-1~{H}-pyrrole-2-carboxamide


Mass: 394.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16ClFN4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10% PEG 8,000, 4% PEG 400, 100 mM imidazole pH 6.6,10 mM spermine, 15 mM MgSO4,100 mM (NH4)2SO4, and 5 mM tris(2-carboxyethyl)phosphine(TCEP)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→47.9 Å / Num. obs: 36440 / % possible obs: 95.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 64.99 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.083 / Rrim(I) all: 0.124 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4427 / CC1/2: 0.523 / Rpim(I) all: 0.924 / Rrim(I) all: 1.409 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIXdev_3051refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.6→47.9 Å / SU ML: 0.4692 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0055 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3099 1795 4.93 %
Rwork0.2479 34632 -
obs0.251 36427 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.31 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7925 0 41 101 8067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00928185
X-RAY DIFFRACTIONf_angle_d1.100211127
X-RAY DIFFRACTIONf_chiral_restr0.05951204
X-RAY DIFFRACTIONf_plane_restr0.00791398
X-RAY DIFFRACTIONf_dihedral_angle_d17.01463090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.35591270.33182652X-RAY DIFFRACTION95.56
2.67-2.750.35481600.32562611X-RAY DIFFRACTION94.99
2.75-2.840.39881190.32552576X-RAY DIFFRACTION92.01
2.84-2.940.38631290.33172687X-RAY DIFFRACTION96.87
2.94-3.060.36071450.32462686X-RAY DIFFRACTION96.42
3.06-3.20.33711420.30672633X-RAY DIFFRACTION95.82
3.2-3.360.3071490.27152642X-RAY DIFFRACTION94.96
3.36-3.570.32751320.27272609X-RAY DIFFRACTION93.1
3.57-3.850.34951310.25472737X-RAY DIFFRACTION97.45
3.85-4.240.30421380.23562681X-RAY DIFFRACTION96.15
4.24-4.850.25451280.21432648X-RAY DIFFRACTION94.42
4.85-6.110.29071430.23192738X-RAY DIFFRACTION96.97
6.11-47.90.28841520.20162732X-RAY DIFFRACTION94.74
Refinement TLS params.Method: refined / Origin x: 203.125851918 Å / Origin y: 0.526408103761 Å / Origin z: 28.7115285003 Å
111213212223313233
T0.446411664542 Å2-0.0542782333899 Å20.0957857759513 Å2-0.46741186149 Å20.0242459354507 Å2--0.550015609212 Å2
L1.12116325261 °2-0.608022238098 °21.23282545876 °2-1.07044766786 °2-0.845792261594 °2--2.27011552277 °2
S0.0477014561016 Å °-0.202803717821 Å °-0.106753703319 Å °0.352681332558 Å °-0.0122299797778 Å °0.017397512108 Å °-0.0303826031749 Å °-0.0671082084837 Å °-0.0311497549669 Å °
Refinement TLS groupSelection details: all

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