5VLZ

Backbone model for phage Qbeta capsid

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

  • Deposited: 2017-04-26 Released: 2017-10-18 
  • Deposition Author(s): Cui, Z., Zhang, J.
  • Funding Organization(s): Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Public Health Service

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of Q beta virions, virus-like particles, and the Q beta-MurA complex reveal internal coat proteins and the mechanism of host lysis.

Cui, Z.Gorzelnik, K.V.Chang, J.Y.Langlais, C.Jakana, J.Young, R.Zhang, J.

(2017) Proc Natl Acad Sci U S A 114: 11697-11702

  • DOI: 10.1073/pnas.1707102114
  • Primary Citation of Related Structures:  
    5VLY, 5VLZ, 5VM7

  • PubMed Abstract: 
  • In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Allolevivirus Qβ the maturation protein, A 2 , has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis ...

    In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Allolevivirus Qβ the maturation protein, A 2 , has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A 2 as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A 2 binding were found to be due to the intimate fit between A 2 and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A 2 , suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX 77843; junjiez@tamu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein
CD [auth AA],
ND [auth AB],
YD [auth AC],
IE [auth AD],
TE [auth AE],
DF [auth AF],
OF [auth AG],
A [auth AH],
L [auth AI],
W [auth AJ],
HA [auth AK],
SA [auth AL],
DB [auth AM],
OB [auth AN],
ZB [auth BA],
KC [auth BB],
RC [auth BC],
SC [auth BD],
TC [auth BE],
UC [auth BF],
VC [auth BG],
WC [auth BH],
XC [auth BI],
YC [auth BJ],
ZC [auth BK],
AD [auth BL],
BD [auth BM],
DD [auth BN],
ED [auth CA],
FD [auth CB],
GD [auth CC],
HD [auth CD],
ID [auth CE],
JD [auth CF],
KD [auth CG],
LD [auth CH],
MD [auth CI],
OD [auth CJ],
PD [auth CK],
QD [auth CL],
RD [auth CM],
SD [auth CN],
TD [auth DA],
UD [auth DB],
VD [auth DC],
WD [auth DD],
XD [auth DE],
ZD [auth DF],
AE [auth DG],
BE [auth DH],
CE [auth DI],
DE [auth DJ],
EE [auth DK],
FE [auth DL],
GE [auth DN],
HE [auth EA],
JE [auth EB],
KE [auth EC],
LE [auth ED],
ME [auth EE],
NE [auth EF],
OE [auth EG],
PE [auth EH],
QE [auth EI],
SE [auth EK],
UE [auth EL],
VE [auth EM],
WE [auth EN],
XE [auth FA],
YE [auth FB],
ZE [auth FC],
AF [auth FD],
BF [auth FE],
CF [auth FF],
EF [auth FH],
FF [auth FI],
GF [auth FJ],
HF [auth FK],
IF [auth FL],
JF [auth FM],
KF [auth FN],
LF [auth GA],
MF [auth GB],
NF [auth GC],
PF [auth GD],
QF [auth GE],
RF [auth GF],
SF [auth GG],
TF [auth GH],
UF [auth GI],
VF [auth GJ],
WF [auth GK],
XF [auth GL],
YF [auth GM],
B [auth GN],
C [auth HA],
D [auth HB],
E [auth HC],
F [auth HD],
G [auth HE],
H [auth HF],
I [auth HG],
J [auth HH],
K [auth HI],
M [auth HJ],
N [auth HK],
O [auth HL],
P [auth HM],
Q [auth HN],
R [auth IA],
S [auth IB],
T [auth IC],
U [auth ID],
V [auth IE],
X [auth IF],
Y [auth IG],
Z [auth IH],
AA [auth II],
BA [auth IJ],
CA [auth IK],
DA [auth IL],
EA [auth IM],
FA [auth IN],
GA [auth JA],
IA [auth JB],
JA [auth JC],
KA [auth JD],
LA [auth JE],
MA [auth JF],
NA [auth JG],
OA [auth JH],
PA [auth JI],
QA [auth JJ],
RA [auth JK],
TA [auth JL],
UA [auth JM],
VA [auth JN],
WA [auth KA],
XA [auth KB],
YA [auth KC],
ZA [auth KD],
AB [auth KE],
BB [auth KF],
CB [auth KG],
EB [auth KH],
FB [auth KI],
GB [auth KJ],
HB [auth KK],
IB [auth KL],
JB [auth KM],
KB [auth KN],
LB [auth LA],
MB [auth LB],
NB [auth LC],
PB [auth LD],
QB [auth LE],
RB [auth LF],
SB [auth LG],
TB [auth LH],
UB [auth LI],
VB [auth LJ],
WB [auth LK],
XB [auth LL],
YB [auth LM],
AC [auth LN],
BC [auth MA],
CC [auth MB],
DC [auth MC],
EC [auth MD],
FC [auth ME],
GC [auth MF],
HC [auth MG],
IC [auth MH],
JC [auth MI],
LC [auth MJ],
MC [auth MK],
NC [auth ML],
OC [auth MM],
PC [auth MN],
QC [auth NA]
133Escherichia virus QbetaMutation(s): 0 
UniProt
Find proteins for P03615 (Escherichia virus Qbeta)
Explore P03615 
Go to UniProtKB:  P03615
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03615
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Maturation protein A2RE [auth EJ]420Escherichia virus QbetaMutation(s): 0 
UniProt
Find proteins for Q8LTE2 (Escherichia virus Qbeta)
Explore Q8LTE2 
Go to UniProtKB:  Q8LTE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LTE2
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-26 
  • Released Date: 2017-10-18 
  • Deposition Author(s): Cui, Z., Zhang, J.

Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesA-1863
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM116787
Public Health ServiceUnited StatesGM27099

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Author supporting evidence, Other
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence, Other