6HAK | pdb_00006hak

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with a double stranded RNA represents the RT transcription initiation complex prior to nucleotide incorporation

• PDB DOI: https://doi.org/10.2210/pdb6HAK/pdb
• NAKB: 6HAK

• Classification: TRANSCRIPTION
• Organism(s): Human immunodeficiency virus type 1 BH10, Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-08-07 Released: 2019-04-03 
• Deposition Author(s): Das, K., Martinez, S.E., Arnold, E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.95 Å
• R-Value Free: 
  0.329 (Depositor), 0.341 (DCC) 
• R-Value Work: 
  0.293 (Depositor), 0.298 (DCC) 
• R-Value Observed: 
  0.296 (Depositor) 

Starting Model: experimental

Literature

Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation.

Das, K., Martinez, S.E., DeStefano, J.J., Arnold, E.

(2019) Proc Natl Acad Sci U S A 116: 7308-7313

• PubMed: 30902895 
• DOI: https://doi.org/10.1073/pnas.1814170116
• Primary Citation Related Structures: 
  6HAK


• PubMed Abstract: 
  

  The initiation phase of HIV reverse transcription has features that are distinct from its elongation phase. The first structure of a reverse transcription initiation complex (RTIC) that trapped the complex after incorporation of one ddCMP nucleotide was published recently [Larsen KP, et al. (2018) Nature 557:118-122]. Here we report a crystal structure of a catalytically active HIV-1 RT/dsRNA complex that mimics the state of the RTIC before the first nucleotide incorporation. The structure reveals that the dsRNA-bound conformation of RT is closer to that of RT bound to a nonnucleoside RT inhibitor (NNRTI) and dsDNA; a hyperextended thumb conformation helps to accommodate the relatively wide dsRNA duplex. The RNA primer 3' end is positioned 5 Å away from the polymerase site; however, unlike in an NNRTI-bound state in which structural elements of RT restrict the movement of the primer, the primer terminus of dsRNA is not blocked from reaching the active site of RT. The observed structural changes and energetic cost of bringing the primer 3' end to the priming site are hypothesized to explain the slower nucleotide incorporation rate of the RTIC. An unusual crystal lattice interaction of dsRNA with its symmetry mate is reminiscent of the RNA architecture within the extended vRNA-tRNA ^Lys3 in the RTIC. This RT/dsRNA complex captures the key structural characteristics and components of the RTIC, including the RT conformational changes and interactions with the dsRNA primer-binding site region, and these features have implications for better understanding of RT initiation.

---

Organizational Affiliation: 
• Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854; [e-mail] [e-mail].
Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854.
Rega Institute, The Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
Department of Microbiology, Immunology and Transplantation, The Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742.
Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 257.97 kDa 
• Atom Count: 17,251 
• Modeled Residue Count: 2,007 
• Deposited Residue Count: 2,080 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	A, E [auth C]	556	Human immunodeficiency virus type 1 BH10	Mutation(s): 3  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	B, F [auth D]	444	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')	C [auth T], G [auth E]	23	Human immunodeficiency virus 1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')	D [auth P], H [auth F]	17	Homo sapiens

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	I [auth G]	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	I [auth G]	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.95 Å
• R-Value Free:  0.329 (Depositor), 0.341 (DCC) 
• R-Value Work:  0.293 (Depositor), 0.298 (DCC) 
• R-Value Observed: 0.296 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.24	α = 90
b = 175.24	β = 90
c = 225.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Das, K., Martinez, S.E., Arnold, E.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37 AI027690

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 2.1: 2022-03-30
  Changes: Author supporting evidence, Database references, Structure summary
• Version 2.2: 2024-01-17
  Changes: Data collection, Refinement description