4BAC | pdb_00004bac

prototype foamy virus strand transfer complexes on product DNA

• PDB DOI: https://doi.org/10.2210/pdb4BAC/pdb
• NAKB: 4BAC

• Classification: TRANSFERASE/DNA
• Organism(s): Human spumaretrovirus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-12 Released: 2012-10-10 
• Deposition Author(s): Yin, Z., Lapkouski, M., Yang, W., Craigie, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.26 Å
• R-Value Free: 
  0.226 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Assembly of Prototype Foamy Virus Strand Transfer Complexes on Product DNA Bypassing Catalysis of Integration.

Yin, Z., Lapkouski, M., Yang, W., Craigie, R.

(2012) Protein Sci 21: 1849

• PubMed: 23011895 
• DOI: https://doi.org/10.1002/pro.2166
• Primary Citation Related Structures: 
  4BAC


• PubMed Abstract: 
  

  Integrase is the key enzyme that mediates integration of retroviral DNA into cellular DNA which is essential for viral replication. Inhibitors of HIV-1 that target integrase recognize the nucleoprotein complexes formed by integrase and viral DNA substrate (intasomes) rather than the free enzyme. Atomic resolution structures of HIV-1 intasomes are therefore required to understand the mechanisms of inhibition and drug resistance. To date, prototype foamy virus (PFV) is the only retrovirus for which such structures have been determined. We show that PFV strand transfer complexes (STC) can be assembled on product DNA without going through the normal forward reaction pathway. The finding that a retroviral STC can be assembled in this way may provide a powerful tool to alleviate the obstacles that impede structural studies of nucleoprotein intermediates in HIV-1 DNA integration.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 112.14 kDa 
• Atom Count: 5,689 
• Modeled Residue Count: 616 
• Deposited Residue Count: 866 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRASE	A, B	396	Human spumaretrovirus	Mutation(s): 0  EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data)
UniProt
Find proteins for P14350 (Human spumaretrovirus) Explore P14350  Go to UniProtKB:  P14350

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'	C	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (38-MER)	D	38	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'	E	17	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.26 Å
• R-Value Free:  0.226 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.617	α = 90
b = 160.617	β = 90
c = 125.092	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Yin, Z., Lapkouski, M., Yang, W., Craigie, R.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references, Other, Structure summary
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description