7LHD

The complete model of phage Qbeta virion

  • Classification: VIRUS/RNA
  • Organism(s): Escherichia virus Qbeta
  • Mutation(s): No 

  • Deposited: 2021-01-22 Released: 2022-01-26 
  • Deposition Author(s): Chang, J.Y., Zhang, J.
  • Funding Organization(s): Welch Foundation, National Science Foundation (NSF, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Assembly of Q beta Virion and Its Diverse Forms of Virus-like Particles.

Chang, J.Y.Gorzelnik, K.V.Thongchol, J.Zhang, J.

(2022) Viruses 14

  • DOI: 10.3390/v14020225
  • Primary Citation of Related Structures:  
    7LGE, 7LGF, 7LGG, 7LGH, 7LHD

  • PubMed Abstract: 
  • The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host ...

    The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3' untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA-RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical T = 3 icosahedral, larger T = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA.


    Organizational Affiliation

    Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Maturation protein A2B [auth M]420Escherichia virus QbetaMutation(s): 0 
UniProt
Find proteins for Q8LTE2 (Escherichia virus Qbeta)
Explore Q8LTE2 
Go to UniProtKB:  Q8LTE2
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UniProt GroupQ8LTE2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein
C [auth B],
E [auth BA],
F [auth BB],
G [auth BC],
H [auth BD],
I [auth BE],
J [auth BF],
K [auth BG],
L [auth BH],
M [auth BI],
N [auth BJ],
O [auth BK],
P [auth BL],
Q [auth BM],
R [auth BN],
S [auth CA],
T [auth CB],
U [auth CC],
V [auth CD],
W [auth CE],
X [auth CF],
Y [auth CG],
Z [auth CH],
AA [auth CI],
BA [auth CJ],
CA [auth CK],
DA [auth CL],
EA [auth CM],
FA [auth CN],
D,
GA [auth DA],
HA [auth DB],
IA [auth DC],
JA [auth DD],
KA [auth DE],
LA [auth DF],
MA [auth DG],
NA [auth DH],
OA [auth DI],
PA [auth DJ],
QA [auth DK],
RA [auth DL],
SA [auth DM],
TA [auth DN],
UA [auth EA],
VA [auth EB],
WA [auth EC],
XA [auth ED],
YA [auth EE],
ZA [auth EF],
AB [auth EG],
BB [auth EH],
CB [auth EI],
DB [auth EJ],
EB [auth EK],
FB [auth EL],
GB [auth EM],
HB [auth EN],
IB [auth FA],
JB [auth FB],
KB [auth FC],
LB [auth FD],
MB [auth FE],
NB [auth FF],
OB [auth FG],
PB [auth FH],
QB [auth FI],
RB [auth FJ],
SB [auth FK],
TB [auth FL],
UB [auth FM],
VB [auth FN],
WB [auth GA],
XB [auth GB],
YB [auth GC],
ZB [auth GD],
AC [auth GE],
BC [auth GF],
CC [auth GG],
DC [auth GH],
EC [auth GI],
FC [auth GJ],
GC [auth GK],
HC [auth GL],
IC [auth GM],
JC [auth GN],
KC [auth HA],
LC [auth HB],
MC [auth HC],
NC [auth HD],
OC [auth HE],
PC [auth HF],
QC [auth HG],
RC [auth HH],
SC [auth HI],
TC [auth HJ],
UC [auth HK],
VC [auth HL],
WC [auth HM],
XC [auth HN],
YC [auth IA],
ZC [auth IB],
AD [auth IC],
BD [auth ID],
CD [auth IE],
DD [auth IF],
ED [auth IG],
FD [auth IH],
GD [auth II],
HD [auth IJ],
ID [auth IK],
JD [auth IL],
KD [auth IM],
LD [auth IN],
MD [auth JA],
ND [auth JB],
OD [auth JC],
PD [auth JD],
QD [auth JE],
RD [auth JF],
SD [auth JG],
TD [auth JH],
UD [auth JI],
VD [auth JJ],
WD [auth JK],
XD [auth JL],
YD [auth JM],
ZD [auth JN],
AE [auth KA],
BE [auth KB],
CE [auth KC],
DE [auth KD],
EE [auth KE],
FE [auth KF],
GE [auth KG],
HE [auth KH],
IE [auth KI],
JE [auth KJ],
KE [auth KK],
LE [auth KL],
ME [auth KM],
NE [auth KN],
OE [auth LA],
PE [auth LB],
QE [auth LC],
RE [auth LD],
SE [auth LE],
TE [auth LF],
UE [auth LG],
VE [auth LH],
WE [auth LI],
XE [auth LJ],
YE [auth LK],
ZE [auth LL],
AF [auth LM],
BF [auth LN],
CF [auth MA],
DF [auth MB],
EF [auth MC],
FF [auth MD],
GF [auth ME],
HF [auth MF],
IF [auth MG],
JF [auth MH],
KF [auth MI],
LF [auth MJ],
MF [auth MK],
NF [auth ML],
OF [auth MM],
PF [auth MN],
QF [auth NA],
RF [auth NB],
SF [auth NC],
TF [auth ND],
UF [auth NE],
VF [auth NF],
WF [auth NG],
XF [auth NH],
YF [auth NI],
ZF [auth NJ]
133Escherichia virus QbetaMutation(s): 0 
UniProt
Find proteins for P03615 (Escherichia virus Qbeta)
Explore P03615 
Go to UniProtKB:  P03615
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UniProt GroupP03615
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Genomic RNAA 4217Escherichia virus Qbeta
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-01-22 
  • Released Date: 2022-01-26 
  • Deposition Author(s): Chang, J.Y., Zhang, J.

Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesA-1863
National Science Foundation (NSF, United States)United StatesMCB-1902392
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI137696
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI095208

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references