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- PDB-3qip: Structure of HIV-1 reverse transcriptase in complex with an RNase... -

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Basic information

Entry
Database: PDB / ID: 3qip
TitleStructure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine
Components
  • Reverse HIV-1 reverse transcriptase p66
  • p51
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / HIV / reverse transcriptase / RNase H / polymerase / nuclease / TRANSFERASE-TRANSFERASE INHIBITOR 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 / host cell plasma membrane / virion membrane / structural molecule activity / 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
: / Chem-NVP / Chem-P4Y / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0926 Å
AuthorsLansdon, E.B. / Kirschberg, T.A.
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 1.2Sep 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_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: Reverse HIV-1 reverse transcriptase p66
B: p51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,96310
Polymers115,9622
Non-polymers1,0018
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-76 kcal/mol
Surface area44530 Å2
MethodPISA
2
A: Reverse HIV-1 reverse transcriptase p66
B: p51
hetero molecules

A: Reverse HIV-1 reverse transcriptase p66
B: p51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,92520
Polymers231,9244
Non-polymers2,00116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area18460 Å2
ΔGint-176 kcal/mol
Surface area83830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.898, 154.876, 153.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Reverse HIV-1 reverse transcriptase p66 / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / PR / Retropepsin / Reverse transcriptase/ribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 64562.949 Da / Num. of mol.: 1 / Fragment: p66 subunit (UNP residues 588-1147)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Gene: gag-pol / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / PR / Retropepsin / Reverse transcriptase/ribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: p51 subunit (UNP Residues 588-1027)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Gene: gag-pol / Plasmid: pET 14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H

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Non-polymers , 6 types, 426 molecules

#3: Chemical ChemComp-NVP / 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE / NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE / Nevirapine


Mass: 266.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O / Comment: medication, antiretroviral*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-P4Y / 5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid


Mass: 361.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15N3O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3M (NH4)2SO4, 5mM sodium malonate, and 100mM cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2007
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.0926→50 Å / Num. obs: 82059 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.3
Reflection shellResolution: 2.0926→2.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 87.9

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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 1VRT

1vrt


Resolution: 2.0926→47.354 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 3822 5.01 %random
Rwork0.2163 ---
obs0.2188 76324 91.7 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.512 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3942 Å2-0 Å20 Å2
2---9.0711 Å2-0 Å2
3---14.4652 Å2
Refinement stepCycle: LAST / Resolution: 2.0926→47.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 61 418 8317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088110
X-RAY DIFFRACTIONf_angle_d1.09111026
X-RAY DIFFRACTIONf_dihedral_angle_d16.2153069
X-RAY DIFFRACTIONf_chiral_restr0.0711191
X-RAY DIFFRACTIONf_plane_restr0.0051383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0926-2.11910.3711660.27831977X-RAY DIFFRACTION67
2.1191-2.1470.34051350.27852183X-RAY DIFFRACTION77
2.147-2.17640.3381150.27382379X-RAY DIFFRACTION81
2.1764-2.20750.35831270.26672411X-RAY DIFFRACTION84
2.2075-2.24050.32011310.262559X-RAY DIFFRACTION88
2.2405-2.27550.29481320.24992493X-RAY DIFFRACTION86
2.2755-2.31280.32611600.25432505X-RAY DIFFRACTION87
2.3128-2.35260.32721500.26462559X-RAY DIFFRACTION89
2.3526-2.39540.3191470.2612600X-RAY DIFFRACTION89
2.3954-2.44150.33531340.27062599X-RAY DIFFRACTION90
2.4415-2.49130.31081500.26582617X-RAY DIFFRACTION90
2.4913-2.54550.34541370.2622647X-RAY DIFFRACTION91
2.5455-2.60470.31581490.25092710X-RAY DIFFRACTION93
2.6047-2.66980.31571450.25472688X-RAY DIFFRACTION92
2.6698-2.7420.35621430.25132718X-RAY DIFFRACTION94
2.742-2.82270.30471600.24332755X-RAY DIFFRACTION95
2.8227-2.91380.28651550.24312800X-RAY DIFFRACTION96
2.9138-3.01790.29811450.23532842X-RAY DIFFRACTION96
3.0179-3.13870.29881450.23412857X-RAY DIFFRACTION97
3.1387-3.28150.25981400.22472858X-RAY DIFFRACTION98
3.2815-3.45450.24241600.21612888X-RAY DIFFRACTION98
3.4545-3.67090.28271560.21032896X-RAY DIFFRACTION99
3.6709-3.95420.24021580.19562929X-RAY DIFFRACTION99
3.9542-4.35180.24191400.18442952X-RAY DIFFRACTION99
4.3518-4.9810.2141420.17232976X-RAY DIFFRACTION100
4.981-6.27320.23221280.2053027X-RAY DIFFRACTION100
6.2732-47.36630.22211720.19493077X-RAY DIFFRACTION99

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