Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 132285.23 
• Atom Count: 8730 
• Residue Count: 1060 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

3KK3

HIV-1 reverse transcriptase-DNA complex with GS-9148 terminated primer

• DOI: 10.2210/pdb3KK3/pdb
• NDB: NA0440

• Classification: TRANSFERASE/DNA
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 3 


• Deposited: 2009-11-04 Released: 2010-03-23 
• Deposition Author(s): Lansdon, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.287 
• R-Value Work: 0.223 

Literature

Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex.

Lansdon, E.B., Samuel, D., Lagpacan, L., Brendza, K.M., White, K.L., Hung, M., Liu, X., Boojamra, C.G., Mackman, R.L., Cihlar, T., Ray, A.S., McGrath, M.E., Swaminathan, S.

(2010) J.Mol.Biol. 397: 967-978

• PubMed: 20156454 
• DOI: 10.1016/j.jmb.2010.02.019
• Primary Citation of Related Structures:  
  3KK2, 3KK1, 3KJV


• PubMed Abstract: 
  

GS-9148 ([5-(6-amino-purin-9-yl)-4-fluoro-2,5-dihydro-furan-2-yloxymethyl]-phosphonic acid) is a dAMP (2'-deoxyadenosine monophosphate) analog that maintains its antiviral activity against drug-resistant HIV. Crystal structures for HIV-1 reverse transcriptase (RT) bound to double-stranded DNA, ternary complexes with either GS-9148-diphosphate or 2'-deoxyadenosine triphosphate (dATP), and a post-incorporation structure with GS-9148 translocated to the priming site were obtained to gain insight into the mechanism of RT inhibition. The binding of either GS-9148-diphosphate or dATP to the binary RT-DNA complex resulted in the fingers subdomain closing around the incoming substrate. This produced up to a 9 A shift in the tips of the fingers subdomain as it closed toward the palm and thumb subdomains. GS-9148-diphosphate shows a similar binding mode as dATP in the nucleotide-binding site. Residues whose mutations confer resistance to nucleotide/nucleoside RT inhibitors, such as M184, Y115, L74, and K65, show little to no shift in orientation whether GS-9148-diphosphate or dATP is bound. One difference observed in binding is the position of the central ring. The dihydrofuran ring of GS-9148-diphosphate interacts with the aromatic side chain of Y115 more than does the ribose ring of dATP, possibly picking up a favorable pi-pi interaction. The ability of GS-9148-diphosphate to mimic the active-site contacts of dATP may explain its effective inhibition of RT and maintained activity against resistance mutations. Interestingly, the 2'-fluoro moiety of GS-9148-diphosphate was found in close proximity to the Q151 side chain, potentially explaining the observed moderately reduced susceptibly to GS-9148 conferred by Q151M mutation.

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Organizational Affiliation: 

Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase p66 subunit	A	560	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 2  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase p51 subunit	B	452	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04585

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*C*(URT))-3'	P	21	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
5'-D(*AP*TP*GP*GP*TP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3'	T	27	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	P, T	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
URT	P	DNA OH 3 prime terminus	C10 H11 F N5 O5 P		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.287 
• R-Value Work: 0.223 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 166.998	α = 90.00
b = 169.070	β = 90.00
c = 96.398	γ = 90.00

Software Package:

Software Name	Purpose
EPMR	phasing
HKL-2000	data scaling
BOS	data collection
HKL-2000	data reduction
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-04 
• Released Date: 2010-03-23 
• Deposition Author(s): Lansdon, E.B.

Revision History 

• Version 1.0: 2010-03-23
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance