1N5Y | pdb_00001n5y

HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P)

• PDB DOI: https://doi.org/10.2210/pdb1N5Y/pdb
• NAKB: 1N5Y

• Classification: TRANSFERASE/IMMUNE SYSTEM/DNA
• Organism(s): Human immunodeficiency virus 1, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-11-07 Released: 2003-01-28 
• Deposition Author(s): Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, P., Ramesha, A.R., Sayer, J.M., Jerina, D.M., Boyer, P.L., Hughes, S.H., Arnold, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.285 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Literature

Structure of HIV-1 Reverse Transcriptase with Pre-Translocation and Post-Translocation AZTMP-Terminated DNA

Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, P., Ramesha, A.R., Sayer, J.M., Jerina, D.M., Boyer, P.L., Hughes, S.H., Arnold, E.

(2002) EMBO J 21: 6614-6624

• PubMed: 12456667 
• DOI: https://doi.org/10.1093/emboj/cdf637
• Primary Citation Related Structures: 
  1N5Y, 1N6Q


• PubMed Abstract: 
  

  AZT (3'-azido-3'-deoxythymidine) resistance involves the enhanced excision of AZTMP from the end of the primer strand by HIV-1 reverse transcriptase. This reaction can occur when an AZTMP-terminated primer is bound at the nucleotide-binding site (pre-translocation complex N) but not at the 'priming' site (post-translocation complex P). We determined the crystal structures of N and P complexes at 3.0 and 3.1 A resolution. These structures provide insight into the structural basis of AZTMP excision and the mechanism of translocation. Docking of a dNTP in the P complex structure suggests steric crowding in forming a stable ternary complex that should increase the relative amount of the N complex, which is the substrate for excision. Structural differences between complexes N and P suggest that the conserved YMDD loop is involved in translocation, acting as a springboard that helps to propel the primer terminus from the N to the P site after dNMP incorporation.

---

Organizational Affiliation: 
• Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 176.78 kDa 
• Atom Count: 12,185 
• Modeled Residue Count: 1,464 
• Deposited Residue Count: 1,472 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE	C [auth A]	558	Human immunodeficiency virus 1	Mutation(s): 2  Gene Names: POL EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE	D [auth B]	430	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: POL EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody (light chain)	E [auth L]	211	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody (heavy chain)	F [auth H]	225	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01868 (Mus musculus) Explore P01868  Go to UniProtKB:  P01868

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*GP*C*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3'	A [auth T]	27	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3'	B [auth P]	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.285 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.7	α = 90
b = 166.7	β = 90
c = 221.12	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-28 
Deposition Author(s): Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, P., Ramesha, A.R., Sayer, J.M., Jerina, D.M., Boyer, P.L., Hughes, S.H., Arnold, E.

Revision History  

• Version 1.0: 2003-01-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary