Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E2F2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A5B3C2D2 

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

Biological Assembly Evidence: gel filtration, fluorescence resonance energy transfer

Macromolecule Content

• Total Structure Weight: 398.46 kDa 
• Atom Count: 21145 
• Residue Count: 2100 
• Unique protein chains: 5
• Unique nucleic acid chains: 5

6RNY

PFV intasome - nucleosome strand transfer complex

• DOI: 10.2210/pdb6RNY/pdb
• EMDataResource: EMD-4960

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, Human spumaretrovirus, Pyrobaculum filamentous virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-05-09 Released: 2019-09-25 
• Deposition Author(s): Pye, V.E., Renault, L., Maskell, D.P., Cherepanov, P., Costa, A.
• Funding Organization(s): The Francis Crick Institute

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.

Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A.

(2019) Nat Commun 10: 4189-4189

• PubMed: 31519882 
• DOI: 10.1038/s41467-019-12007-w
• Primary Citation of Related Structures:  
  6R0C, 6RNY


• PubMed Abstract: 
  

Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers.

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Related Citations: 

• Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.
  Wilson, M.D., Renault, L., Maskell, D.P., Ghoneim, M., Pye, V.E., Nans, A., Rueda, D.S., Cherepanov, P., Costa, A.
  (2019) Nat Commun 10: 4189

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Organizational Affiliation: 

Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	A, E	136	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS:  P84243 GTEx:  ENSG00000163041

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS:  P62805 GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H2AG, H2AFP, HIST1H2AI, H2AFC, HIST1H2AK, H2AFD, HIST1H2AL, H2AFI, HIST1H2AM, H2AFN, H2AC11, H2AC13, H2AC15, H2AC16, H2AC17
Find proteins for P0C0S8 (Homo sapiens) Explore P0C0S8  Go to UniProtKB:  P0C0S8
NIH Common Fund Data Resources
PHAROS:  P0C0S8 GTEx:  ENSG00000196747ENSG00000196787ENSG00000278677ENSG00000276903

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-C/E/F/G/I	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK, H2BC4, H2BC6, H2BC7, H2BC8, H2BC10
Find proteins for P62807 (Homo sapiens) Explore P62807  Go to UniProtKB:  P62807
NIH Common Fund Data Resources
PHAROS:  P62807 GTEx:  ENSG00000180596ENSG00000277224ENSG00000278588ENSG00000273802ENSG00000274290

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	K, L, O, P	395	Human spumaretrovirus	Mutation(s): 2  Gene Names: pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 3.4.23 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
Find proteins for P14350 (Human spumaretrovirus) Explore P14350  Go to UniProtKB:  P14350

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (128-MER)	I	128	Homo sapiens

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (108-MER)	U	108	Homo sapiens

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	T	33	Homo sapiens

Entity ID: 9
Molecule	Chains	Length	Organism	Image
DNA (53-MER)	J	53	Homo sapiens

Entity ID: 10
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')	M, Q	19	Pyrobaculum filamentous virus 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	K, O	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-05-09 
• Released Date: 2019-09-25 
Deposition Author(s): Pye, V.E., Renault, L., Maskell, D.P., Cherepanov, P., Costa, A.

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Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC0010061
The Francis Crick Institute	United Kingdom	FC0010065

Revision History 

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Other