Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ.
Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2and the gRNA. A2contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.
Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.
Karl V
KV
Gorzelnik
Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.
Zhicheng
Z
Cui
Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.
Catrina A
CA
Reed
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.
Joanita
J
Jakana
Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.
Ry
R
Young
Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843; junjiez@tamu.edu.
Junjie
J
Zhang
D017908:Allolevivirus / Q000648:ultrastructure*; D002213:Capsid / Q000737:chemistry; D036022:Capsid Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D020832:EF Hand Motifs; D016679:Genome, Viral; D008958:Models, Molecular; D055503:Protein Multimerization; D012367:RNA, Viral / Q000737:chemistry* / Q000648:ultrastructure*
D036022:Capsid Proteins; D012367:RNA, Viral
Allolevivirus; genomic RNA; maturation protein; single-particle cryo-EM; ssRNA virus
Biochem J. 2014 Sep 1;462(2):215-30
25102029
Nat Methods. 2012 Sep;9(9):853-4
22842542
J Mol Biol. 2001 May 18;308(5):1033-44
11352589
IEEE NIH Life Sci Syst Appl Workshop. 2009 Apr 1;2009:44-47
20556220
Biochim Biophys Acta. 1974 Dec 6;374(2):238-51
4611493
J Mol Biol. 1993 Dec 5;234(3):620-39
8254664
J Mol Biol. 2008 Jan 18;375(3):824-36
18048058
Mol Microbiol. 2012 Nov;86(4):836-44
22934834
Virology. 1970 Apr;40(4):920-9
4914647
J Mol Biol. 2011 May 6;408(3):399-407
21354423
Nature. 2006 Feb 2;439(7076):612-6
16452981
J Struct Biol. 2007 Jan;157(1):3-18
17011211
Virology. 2015 May;479-480:2-25
25771806
Structure. 2013 Jul 2;21(7):1225-34
23810697
J Struct Biol. 2012 Dec;180(3):519-30
23000701
Methods. 2009 Oct;49(2):174-80
19398010
Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2654-9
26929357
Elife. 2015 May 29;4:e06980
26023829
Nature. 1994 Oct 13;371(6498):623-6
7523953
J Struct Biol. 2007 Jan;157(1):38-46
16859925
Biophys J. 2011 Aug 17;101(4):774-80
21843467
J Struct Biol. 1999 Dec 1;128(1):82-97
10600563
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
8744570
J Comput Chem. 2004 Oct;25(13):1605-12
15264254
Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17174-8
17090672
J Struct Biol. 2016 Jan;193(1):1-12
26592709
J Struct Biol. 2015 Nov;192(2):216-21
26278980
Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21
20057044
Science. 2004 Mar 5;303(5663):1526-9
14976262
J Virol. 2012 Aug;86(15):7806-17
22593159
J Mol Biol. 1995 Apr 14;247(5):903-17
7723040
RNA. 1998 Aug;4(8):948-57
9701286
Biochim Biophys Acta. 1981 Jul 27;654(2):249-55
6974569
Nat Methods. 2015 Jan;12(1):7-8
25549265
Protein Sci. 2011 Oct;20(10):1707-12
21805520
Science. 1965 Apr 23;148(3669):511-3
14263773
J Mol Biol. 2016 Jan 29;428(2 Pt B):431-48
26608810
Bacteriophage. 2016 Mar 2;6(1):e1157666
27144089
Antivir Chem Chemother. 2003 Mar;14(2):61-73
12856917
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
20383002
J Mol Biol. 1996 Feb 16;256(1):8-19
8609616
Science. 2006 Jun 23;312(5781):1791-5
16709746
Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5361-6
24706827
Nat Methods. 2013 Jun;10(6):584-90
23644547
J Mol Biol. 1963 Jul;7:43-54
13978804
J Struct Biol. 2005 Oct;152(1):36-51
16182563
Microbiology (Reading). 2013 Mar;159(Pt 3):507-514
23329676
RNA. 2015 Apr;21(4):667-9
25780183
Science. 2001 Jun 22;292(5525):2326-9
11423662
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
20124702
J Mol Biol. 2003 Sep 12;332(2):415-22
12948491
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1355-60
21220301
J Mol Biol. 2010 Aug 13;401(2):309-322
20684044
J Mol Biol. 2014 Mar 6;426(5):1039-49
24035813
Structure. 1996 May 15;4(5):543-54
8736553