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- PDB-6bsh: Structure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hy... -

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Basic information

Entry
Database: PDB / ID: 6bsh
TitleStructure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hydrolysis 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 / RNase H / 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 / 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 / DNA integration / 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 / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / 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-EFZ / DNA / DNA (> 10) / RNA / RNA (> 10) / Pol protein / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.649 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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

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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)131,60414
Polymers130,4934
Non-polymers1,11210
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15380 Å2
ΔGint-109 kcal/mol
Surface area47480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.792, 161.792, 128.773
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 / Pr160Gag-Pol


Mass: 64126.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03367, UniProt: P04585*PLUS, DNA-directed DNA polymerase
#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, 125 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
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, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→37.2 Å / Num. obs: 56790 / % possible obs: 99.91 % / Redundancy: 6.2 % / Rsym value: 0.076 / Net I/σ(I): 19.94
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.04 / Num. unique obs: 5625 / % possible all: 99.75

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.649→37.204 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2002 3.53 %
Rwork0.1892 --
obs0.1905 56770 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.649→37.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7670 989 70 115 8844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099081
X-RAY DIFFRACTIONf_angle_d1.04912569
X-RAY DIFFRACTIONf_dihedral_angle_d17.8765293
X-RAY DIFFRACTIONf_chiral_restr0.0541395
X-RAY DIFFRACTIONf_plane_restr0.0071416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6488-2.7150.3691400.27933869X-RAY DIFFRACTION100
2.715-2.78840.30641440.2763875X-RAY DIFFRACTION100
2.7884-2.87040.37771420.26673860X-RAY DIFFRACTION100
2.8704-2.9630.36591450.26713874X-RAY DIFFRACTION100
2.963-3.06890.30541410.26683870X-RAY DIFFRACTION100
3.0689-3.19170.29481420.23423891X-RAY DIFFRACTION100
3.1917-3.33690.23241390.21713920X-RAY DIFFRACTION100
3.3369-3.51270.29621410.20933889X-RAY DIFFRACTION100
3.5127-3.73260.23471400.20023886X-RAY DIFFRACTION100
3.7326-4.02050.26451420.18193913X-RAY DIFFRACTION100
4.0205-4.42450.20041460.15833938X-RAY DIFFRACTION100
4.4245-5.06330.17051450.15213941X-RAY DIFFRACTION100
5.0633-6.3740.19471470.17813968X-RAY DIFFRACTION100
6.374-37.20760.18391480.16734074X-RAY DIFFRACTION99

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