Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 176.88 kDa 
• Atom Count: 12292 
• Residue Count: 1467 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

1R0A

Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms

• DOI: 10.2210/pdb1R0A/pdb
• NDB: PD0472

• Classification: Transferase/immune system/DNA
• Organism(s): Human immunodeficiency virus 1, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-09-19 Released: 2004-08-03 
• Deposition Author(s): Tuske, S., Ding, J., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.272 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA.

Peletskaya, E.N., Kogon, A.A., Tuske, S., Arnold, E., Hughes, S.H.

(2004) J Virol 78: 3387-3397

• PubMed: 15016861 
• DOI: 10.1128/jvi.78.7.3387-3397.2004
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Site-directed photoaffinity cross-linking experiments were performed by using human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) mutants with unique cysteine residues at several positions (i.e., positions 65, 67, 70, and 74) in the fingers subdomain of the p66 subunit. Since neither the introduction of the unique cysteine residues into the fingers nor the modification of the SH groups of these residues with photoaffinity cross-linking reagents caused a significant decrease in the enzymatic activities of RT, we were able to use this system to measure distances between specific positions in the fingers domain of RT and double-stranded DNA. HIV-1 RT is quite flexible. There are conformational changes associated with binding of the normal substrates and nonnucleoside RT inhibitors (NNRTIs). Cross-linking was used to monitor intramolecular movements associated with binding of an NNRTI either in the presence or in the absence of an incoming deoxynucleoside triphosphate (dNTP). Binding an incoming dNTP at the polymerase active site decreased the efficiency of cross-linking but caused only modest changes in the preferred positions of cross-linking. This finding suggests that the fingers of p66 are closer to an extended template in the "open" configuration of the enzyme with the fingers away from the active site than in the closed configuration with the fingers in direct contact with the incoming dNTP. NNRTI binding caused increased cross-linking in experiments with diazirine reagents (especially with a diazirine reagent with a longer linker) and a moderate shift in the preferred sites of interaction with the template. Cross-linking occurred closer to the polymerase active site for RTs modified at positions 70 and 74. The effects of NNRTI binding were more pronounced in the absence of a bound dNTP; pretreatment of HIV-1 RT with an NNRTI reduced the effect of dNTP binding. These observations can be explained if the binding of NNRTI causes a decrease in the flexibility in the fingers subdomain of RT-NNRTI complex and a decrease in the distance from the fingers to the template extension.

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Organizational Affiliation: 

HIV Drug Resistance Program. SAIC Frederick, National Cancer Institute at Frederick, Frederick, Maryland 21702-1201, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase	A	558	Human immunodeficiency virus 1	Mutation(s): 2  Gene Names: POL EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Go to UniProtKB:  P03366

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase	B	429	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: POL EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Go to UniProtKB:  P03366

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
monoclonal antibody (light chain)	L	211	Mus musculus	Mutation(s): 0

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(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*GP*GP*T)-3'	T	27	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*C*CP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*AP*GP*CP*GP*CP*CP*GP*(2DA))-3'	P	21	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	H	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
GOL	B, P	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.272 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.82	α = 90
b = 165.82	β = 90
c = 220.72	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-19 
• Released Date: 2004-08-03 
Deposition Author(s): Tuske, S., Ding, J., Arnold, E.

Revision History 

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance