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- PDB-3qio: Crystal Structure of HIV-1 RNase H with engineered E. coli loop a... -

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Basic information

Entry
Database: PDB / ID: 3qio
TitleCrystal Structure of HIV-1 RNase H with engineered E. coli loop and N-hydroxy quinazolinedione inhibitor
ComponentsGag-Pol polyprotein,Ribonuclease HI,Gag-Pol polyprotein
KeywordsTRANSFERASE / HYDROLASE/INHIBITOR / RNase H / HIV-1 / inhibitor / nuclease / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


DNA replication, removal of RNA primer / integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs ...DNA replication, removal of RNA primer / integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / Assembly Of The HIV Virion / exoribonuclease H / exoribonuclease H activity / 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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / viral nucleocapsid / endonuclease activity / DNA recombination / nucleic acid binding / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / magnesium ion binding / DNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Ribonuclease HI / : / 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 ...Ribonuclease HI / : / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-QID / Gag-Pol polyprotein / Ribonuclease HI
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4011 Å
AuthorsLansdon, E.B. / Liu, Q.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2011
Title: Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors.
Authors: Lansdon, E.B. / Liu, Q. / Leavitt, S.A. / Balakrishnan, M. / Perry, J.K. / Lancaster-Moyer, C. / Kutty, N. / Liu, X. / Squires, N.H. / Watkins, W.J. / Kirschberg, T.A.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag-Pol polyprotein,Ribonuclease HI,Gag-Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4465
Polymers16,9211
Non-polymers5244
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.905, 56.352, 64.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gag-Pol polyprotein,Ribonuclease HI,Gag-Pol polyprotein / Pr160Gag-Pol / RNase HI / Ribonuclease H / RNase H / Pr160Gag-Pol


Mass: 16921.463 Da / Num. of mol.: 1
Fragment: HIV-1 RNase H (UNP REsdieus 1014-1148),HIV-1 RNase H (UNP REsdieus 1014-1148),HIV-1 RNase H (UNP REsdieus 1014-1148)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B, (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2, K12 / Gene: gag-pol, rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 / Plasmid: pET 30B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04585, UniProt: P0A7Y4, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring ...References: UniProt: P04585, UniProt: P0A7Y4, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds, ribonuclease H
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-QID / 3-hydroxy-6-(phenylsulfonyl)quinazoline-2,4(1H,3H)-dione


Mass: 318.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10N2O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 100mM HEPES pH 7.5, and 200mM LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2007
RadiationMonochromator: single crystal, cylindrically bent, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 30610 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.3
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.7 / % possible all: 83.1

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HRH

1hrh


Resolution: 1.4011→28.176 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1903 6.55 %random
Rwork0.1958 ---
obs0.1978 29060 93.12 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.216 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2908 Å20 Å2-0 Å2
2--3.3656 Å20 Å2
3----3.6565 Å2
Refinement stepCycle: LAST / Resolution: 1.4011→28.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 29 185 1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051123
X-RAY DIFFRACTIONf_angle_d0.9321525
X-RAY DIFFRACTIONf_dihedral_angle_d11.809419
X-RAY DIFFRACTIONf_chiral_restr0.065173
X-RAY DIFFRACTIONf_plane_restr0.003189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4011-1.43610.3814960.30821404X-RAY DIFFRACTION69
1.4361-1.47490.31571160.28191673X-RAY DIFFRACTION81
1.4749-1.51830.30551270.25341815X-RAY DIFFRACTION89
1.5183-1.56730.26741370.21941898X-RAY DIFFRACTION92
1.5673-1.62330.23751350.21651927X-RAY DIFFRACTION94
1.6233-1.68830.25911340.20981946X-RAY DIFFRACTION94
1.6883-1.76520.26921400.21471983X-RAY DIFFRACTION96
1.7652-1.85820.23851410.19511985X-RAY DIFFRACTION96
1.8582-1.97460.25311420.19022018X-RAY DIFFRACTION97
1.9746-2.1270.21441450.18482077X-RAY DIFFRACTION99
2.127-2.3410.19121450.17552070X-RAY DIFFRACTION99
2.341-2.67950.2331480.17692100X-RAY DIFFRACTION100
2.6795-3.3750.20981480.19082122X-RAY DIFFRACTION100
3.375-28.18170.22391490.19922139X-RAY DIFFRACTION96

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