4MH8 | pdb_00004mh8

The crystal structure of the monomeric reverse transcriptase from moloney murine leukemia virus

• PDB DOI: https://doi.org/10.2210/pdb4MH8/pdb
• Entry: 4MH8 supersedes: 1RW3

• Classification: TRANSFERASE, HYDROLASE, REPLICATION
• Organism(s): Moloney murine leukemia virus isolate Shinnick
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-08-29 Released: 2013-10-16 
• Deposition Author(s): Das, D., Georgiadis, M.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.277 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Models: experimental

Literature

The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.

Das, D., Georgiadis, M.M.

(2004) Structure 12: 819-829

• PubMed: 15130474 
• DOI: https://doi.org/10.1016/j.str.2004.02.032
• Primary Citation Related Structures: 
  4MH8


• PubMed Abstract: 
  

  Reverse transcriptases (RTs) are multidomain enzymes of variable architecture that couple both RNA- and DNA-directed DNA polymerase activities with an RNase H activity specific for an RNA:DNA hybrid in order to replicate the single-stranded RNA genome of the retrovirus. Previous structural work has been reported for the heterodimeric HIV-1 and HIV-2 RTs. We now report the first crystal structure of the full-length Moloney murine leukemia virus (MMLV) RT at 3.0 A resolution. The structure reveals a clamp-shaped molecule resulting from the relative positions of the thumb, connection, and RNase H domains that is strikingly different from the HIV-1 RT and provides the first example of a monomeric reverse transcriptase. A comparative analysis with related DNA polymerases suggests a unique trajectory for the template-primer exiting the polymerase active site and provides insights regarding processive DNA synthesis by MMLV RT.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 72.57 kDa 
• Atom Count: 3,580 
• Modeled Residue Count: 453 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H p80	A	652	Moloney murine leukemia virus isolate Shinnick	Mutation(s): 1  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick)) Explore P03355  Go to UniProtKB:  P03355

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.277 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.332	α = 90
b = 94.621	β = 90
c = 52.408	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
MLPHARE	phasing
PHASER	phasing
PHENIX	model building
AMoRE	phasing
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Das, D., Georgiadis, M.M.
• This entry supersedes: 1RW3

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description