Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 177114.36 
• Atom Count: 12248 
• Residue Count: 1473 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

1N6Q

HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N)

• DOI: 10.2210/pdb1N6Q/pdb
• NDB: PD0364

• Classification: TRANSFERASE/IMMUNE SYSTEM/DNA
• Organism(s): Human immunodeficiency virus type 1 group M subtype B, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2002-11-11 Released: 2003-01-14 
• Deposition Author(s): Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, I., 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 Å
• R-Value Free: 0.284 
• R-Value Work: 0.247 

Literature

Structures of HIV-1 Reverse Transcriptase with Pre- and Post-translocation AZTMP-terminated DNA

Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, I., 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 
• Primary Citation of Related Structures:  
  1N5Y


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Reverse Transcriptase	A	558	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 2  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03366

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Reverse Transcriptase	B	430	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03366

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Monoclonal Antibody (Light Chain)	L	211	Mus musculus	Mutation(s): 0
Find proteins for I6L991 (Mus musculus) Go to UniProtKB:  I6L991

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Monoclonal Antibody (Heavy Chain)	H	225	Mus musculus	Mutation(s): 0  Gene Names: Ighg1 (Igh-4)
Find proteins for P01868 (Mus musculus) Go to UniProtKB:  P01868

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*AP*T*GP*CP*AP*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

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*AP*(ATM))-3'	P	22	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ATM	P	DNA LINKING	C10 H14 N5 O7 P		DT
MRG	P	DNA LINKING	C13 H20 N5 O7 P S		DG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.284 
• R-Value Work: 0.247 
• Space Group: P 3₂ 1 2

Unit Cell:

Length (Å)	Angle (°)
a = 166.350	α = 90.00
b = 166.350	β = 90.00
c = 220.960	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-11 
• Released Date: 2003-01-14 
• Deposition Author(s): Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, I., Ramesha, A.R., Sayer, J.M., Jerina, D.M., Boyer, P.L., Hughes, S.H., Arnold, E.

Revision History 

• Version 1.0: 2003-01-14
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance