6BHJ

Structure of HIV-1 Reverse Transcriptase Bound to a 38-mer Hairpin Template-Primer RNA-DNA Aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Integrative Structural Biology Studies of HIV-1 Reverse Transcriptase Binding to a High-Affinity DNA Aptamer

Tuske, S.Zheng, J.Olson, E.D.Ruiz, F.X.Pascal, B.D.Bauman, J.D.Das, K.DeStefano, J.J.Musier-Forsyth, K.Griffin, P.R.Arnold, E.

(2020) Curr Res Struct Biol 


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE P66 subunit
A, C
557Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE P51 subunit
B, D
444Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
38-MER RNA-DNA Aptamer
E, F
38synthetic construct
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
G, H
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
L [auth B]
M [auth B]
O [auth C]
J [auth B],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
P [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.055α = 90
b = 127.463β = 101.81
c = 132.125γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIGMS P50 GM103368

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-07-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary