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- PDB-5i3u: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE N-SITE COMPLEX; CATALYTI... -

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Basic information

Entry
Database: PDB / ID: 5i3u
TitleSTRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE N-SITE COMPLEX; CATALYTIC INCORPORATION OF AZTMP to A DNA aptamer in CRYSTAL
Components
  • (HIV-1 REVERSE TRANSCRIPTASE ...) x 2
  • DNA (39-MER)
KeywordsTRANSFERASE/DNA / RT / DNA APTAMER / Foscavir / N site complex / pyrophosphate / pyrophosphorolysis / phosphonoformic acid / PFA / 2-O-METHYLCYTIDINE / P51 / P66 / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion 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 / 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDas, K. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI027690 United States
Citation
Journal: Acs Chem.Biol. / Year: 2016
Title: Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.
Authors: Das, K. / Balzarini, J. / Miller, M.T. / Maguire, A.R. / DeStefano, J.J. / Arnold, E.
#1: Journal: Protein Sci. / Year: 2016
Title: Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer
Authors: Miller, M.T.
#2: Journal: PROC.NATL.ACAD.SCI.USA / Year: 2015
Title: Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics
Authors: Balzarini, J.
#3: Journal: Nat. Struct. Mol. Biol. / Year: 2012
Title: HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
Authors: Miller, M.T. / Tuske, S. / Das, K. / DeStefano, J.J. / Arnold, E.
#4: Journal: Nat. Struct. Mol. Biol. / Year: 2010
Title: Structural basis of HIV-1 resistance to AZT by excision.
Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (39-MER)
F: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,68012
Polymers255,7636
Non-polymers9176
Water00
1
A: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4327
Polymers127,8813
Non-polymers5514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13370 Å2
ΔGint-35 kcal/mol
Surface area46170 Å2
MethodPISA
2
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
F: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2485
Polymers127,8813
Non-polymers3672
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-37 kcal/mol
Surface area46930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.240, 128.710, 131.660
Angle α, β, γ (deg.)90.00, 100.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HIV-1 REVERSE TRANSCRIPTASE ... , 2 types, 4 molecules ACBD

#1: Protein HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT / Pr160Gag-Pol


Mass: 63875.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT / Pr160Gag-Pol


Mass: 51928.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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DNA chain / Sugars , 2 types, 4 molecules EF

#3: DNA chain DNA (39-MER)


Mass: 12077.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 7% PEG 8000, 25 MM BISTRIS-PROPANE PH 6.8, 75 MM BISTRIS-PROPANE PH 7.4, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE
PH range: 6.8 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→48.1 Å / Num. obs: 58402 / % possible obs: 98.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 77.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.8
Reflection shellResolution: 3→3.08 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G

5d3g


Resolution: 3→48.1 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.61
RfactorNum. reflection% reflection
Rfree0.254 2342 4.01 %
Rwork0.2231 --
obs0.2244 58346 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15787 1484 60 0 17331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417981
X-RAY DIFFRACTIONf_angle_d0.62224720
X-RAY DIFFRACTIONf_dihedral_angle_d14.76710521
X-RAY DIFFRACTIONf_chiral_restr0.0432698
X-RAY DIFFRACTIONf_plane_restr0.0042857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.06120.4581290.37833266X-RAY DIFFRACTION99
3.0612-3.12780.39151270.34363298X-RAY DIFFRACTION98
3.1278-3.20050.29851280.31033259X-RAY DIFFRACTION99
3.2005-3.28060.31871440.28343286X-RAY DIFFRACTION98
3.2806-3.36930.29121360.26893262X-RAY DIFFRACTION98
3.3693-3.46840.28081340.27243281X-RAY DIFFRACTION98
3.4684-3.58030.34351500.26853245X-RAY DIFFRACTION99
3.5803-3.70820.31561250.27053294X-RAY DIFFRACTION98
3.7082-3.85670.29841360.24083298X-RAY DIFFRACTION99
3.8567-4.03210.26251500.23033292X-RAY DIFFRACTION99
4.0321-4.24460.21381440.21943288X-RAY DIFFRACTION99
4.2446-4.51040.26091370.2063292X-RAY DIFFRACTION98
4.5104-4.85850.21351390.20083293X-RAY DIFFRACTION99
4.8585-5.3470.24371560.19663291X-RAY DIFFRACTION99
5.347-6.11970.26781350.21943325X-RAY DIFFRACTION99
6.1197-7.70630.24211490.20693328X-RAY DIFFRACTION99
7.7063-52.62180.17361230.17243406X-RAY DIFFRACTION99

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