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- PDB-3qin: Crystal Structure of HIV-1 RNase H p15 with engineered E. coli lo... -

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Entry
Database: PDB / ID: 3qin
TitleCrystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor
ComponentsFusion protein of HIV-1 RNase H p15 with engineered E. coli loop
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 / : / : / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / Budding and maturation of HIV virion / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / DNA recombination / nucleic acid binding / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding / 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 / Integrase DNA binding domain ...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. / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-P1Y / 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 / MOLECULAR REPLACEMENT / Resolution: 1.6967 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 1.2May 31, 2017Group: Database references
Revision 1.3Jan 13, 2021Group: Derived calculations / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_name_com.name / _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
Revision 1.4Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description
Revision 1.5Sep 13, 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: Fusion protein of HIV-1 RNase H p15 with engineered E. coli loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4835
Polymers16,9211
Non-polymers5614
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.841, 90.370, 111.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-5-

HOH

21A-58-

HOH

31A-62-

HOH

41A-152-

HOH

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Components

#1: Protein Fusion protein of HIV-1 RNase H p15 with engineered E. coli loop / / Pr160Gag-Pol / RNase HI / Ribonuclease H / RNase H


Mass: 16921.463 Da / Num. of mol.: 1 / Fragment: HIV-1 RNase H
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-P1Y / 2-(3-bromo-4-methoxybenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid


Mass: 355.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11BrN2O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M (NH4)2SO4, 100mM HEPES pH 7.5, and 3% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6967→50 Å / Num. obs: 21540 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.6
Reflection shellResolution: 1.6967→1.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 95

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Processing

Software
NameVersionClassification
CrystalCleardata 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: 1.6967→23.118 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1932 9.26 %random
Rwork0.2203 ---
obs0.2233 20866 93.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.68 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.2293 Å2-0 Å20 Å2
2---8.2099 Å20 Å2
3----5.0194 Å2
Refinement stepCycle: LAST / Resolution: 1.6967→23.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 28 153 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081124
X-RAY DIFFRACTIONf_angle_d1.1371523
X-RAY DIFFRACTIONf_dihedral_angle_d13.902416
X-RAY DIFFRACTIONf_chiral_restr0.11174
X-RAY DIFFRACTIONf_plane_restr0.005190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6967-1.73910.33511180.32871155X-RAY DIFFRACTION82
1.7391-1.78610.34421270.29441249X-RAY DIFFRACTION88
1.7861-1.83860.28631280.25751277X-RAY DIFFRACTION90
1.8386-1.89790.23691330.21371313X-RAY DIFFRACTION92
1.8979-1.96570.23621330.20111356X-RAY DIFFRACTION94
1.9657-2.04440.23011410.20491345X-RAY DIFFRACTION94
2.0444-2.13740.25021410.21131365X-RAY DIFFRACTION96
2.1374-2.250.27551430.21711383X-RAY DIFFRACTION97
2.25-2.39080.24741410.21811375X-RAY DIFFRACTION96
2.3908-2.57520.21421460.2051417X-RAY DIFFRACTION97
2.5752-2.83390.2911430.19881398X-RAY DIFFRACTION98
2.8339-3.2430.23231450.21681426X-RAY DIFFRACTION97
3.243-4.08220.2131450.19891427X-RAY DIFFRACTION97
4.0822-23.12010.29081480.24791448X-RAY DIFFRACTION93

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