[English] 日本語
Yorodumi
- PDB-5i3u: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE N-SITE COMPLEX; CATALYTI... -

+
Open data


ID or keywords:

Loading...

-
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 ...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 / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / 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 / 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 / proteolysis / DNA binding / RNA 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. / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

-
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

-
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

-
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 / Glycerol


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more