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- PDB-6bsg: Structure of HIV-1 RT complexed with RNA/DNA hybrid in an RNA hyd... -

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Basic information

Entry
Database: PDB / ID: 6bsg
TitleStructure of HIV-1 RT complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode
Components
  • (REVERSE TRANSCRIPTASE ...) x 2
  • DNA (5'-D(*GP*TP*AP*TP*GP*CP*CP*AP*CP*TP*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3')
  • RNA (25-MER)
Keywordsviral protein/dna/rna/inhibitor / HIV-RT / DNA-RNA complex / VIRAL PROTEIN / viral protein-dna-rna complex / viral protein-dna-rna-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 / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Budding and maturation of HIV virion / host multivesicular body / protein processing / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / 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 / 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 / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / identical protein binding / membrane
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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EFZ / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / RNA / RNA (> 10) / Pol protein / Gag-Pol polyprotein / Pol
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å
AuthorsTian, L. / Kim, M. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid.
Authors: Tian, L. / Kim, M.S. / Li, H. / Wang, J. / Yang, W.
History
DepositionDec 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE P66 SUBUNIT
B: REVERSE TRANSCRIPTASE P51 SUBUNIT
D: DNA (5'-D(*GP*TP*AP*TP*GP*CP*CP*AP*CP*TP*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3')
R: RNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,36312
Polymers130,4934
Non-polymers8708
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-101 kcal/mol
Surface area48420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.040, 162.040, 129.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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REVERSE TRANSCRIPTASE ... , 2 types, 2 molecules AB

#1: Protein REVERSE TRANSCRIPTASE P66 SUBUNIT


Mass: 64126.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q74085, UniProt: P04585*PLUS
#2: Protein REVERSE TRANSCRIPTASE P51 SUBUNIT


Mass: 51384.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076Q3N8, UniProt: P04585*PLUS

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DNA chain / RNA chain , 2 types, 2 molecules DR

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


Mass: 7062.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: RNA chain RNA (25-MER)


Mass: 7919.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 140 molecules

#5: Chemical ChemComp-EFZ / (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE / DMP-266 / Efavirenz


Mass: 315.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9ClF3NO2 / Comment: medication, antiretroviral*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate pH 5.2, CaCl2, PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→40.51 Å / Num. obs: 72938 / % possible obs: 100 % / Redundancy: 7.4 % / Rsym value: 0.081 / Net I/σ(I): 13.49
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 6.4 % / Num. unique obs: 7221 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.44→40.51 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 3848 2.73 %
Rwork0.1907 --
obs0.1917 140951 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7728 989 54 132 8903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079107
X-RAY DIFFRACTIONf_angle_d0.94812589
X-RAY DIFFRACTIONf_dihedral_angle_d17.9425319
X-RAY DIFFRACTIONf_chiral_restr0.051395
X-RAY DIFFRACTIONf_plane_restr0.0051415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.47090.33161420.30725035X-RAY DIFFRACTION100
2.4709-2.50340.31211420.29625100X-RAY DIFFRACTION100
2.5034-2.53770.28611440.27565080X-RAY DIFFRACTION100
2.5377-2.5740.37331410.2685113X-RAY DIFFRACTION100
2.574-2.61240.26291410.26645072X-RAY DIFFRACTION100
2.6124-2.65320.30241440.25185079X-RAY DIFFRACTION100
2.6532-2.69670.27271430.24785135X-RAY DIFFRACTION100
2.6967-2.74320.2861420.24825031X-RAY DIFFRACTION100
2.7432-2.7930.31631470.25075090X-RAY DIFFRACTION100
2.793-2.84670.33971420.25115093X-RAY DIFFRACTION100
2.8467-2.90480.3141410.25315035X-RAY DIFFRACTION100
2.9048-2.9680.28981450.24665090X-RAY DIFFRACTION100
2.968-3.0370.30811440.24725061X-RAY DIFFRACTION100
3.037-3.11290.23971450.24255143X-RAY DIFFRACTION100
3.1129-3.19710.31091450.23335075X-RAY DIFFRACTION100
3.1971-3.29110.28841430.22715094X-RAY DIFFRACTION100
3.2911-3.39730.2441410.21425091X-RAY DIFFRACTION100
3.3973-3.51860.24131440.20625081X-RAY DIFFRACTION100
3.5186-3.65940.21981410.19435024X-RAY DIFFRACTION100
3.6594-3.82580.20821370.18955102X-RAY DIFFRACTION100
3.8258-4.02740.20881450.17455042X-RAY DIFFRACTION100
4.0274-4.27940.1991440.16155101X-RAY DIFFRACTION100
4.2794-4.60940.1741400.15495067X-RAY DIFFRACTION99
4.6094-5.07250.21121390.15345073X-RAY DIFFRACTION100
5.0725-5.80470.19951400.16135054X-RAY DIFFRACTION100
5.8047-7.30630.21231430.17965076X-RAY DIFFRACTION100
7.3063-40.51560.16091430.15755066X-RAY DIFFRACTION99

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