8UEJ

ssRNA phage PhiCb5 virion

  • Classification: VIRUS
  • Organism(s): Caulobacter phage phiCb5
  • Mutation(s): No 

  • Deposited: 2023-10-01 Released: 2024-05-15 
  • Deposition Author(s): Wang, Y., Zhang, J.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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 mechanisms of Tad pilus assembly and its interaction with an RNA virus.

Wang, Y.Theodore, M.Xing, Z.Narsaria, U.Yu, Z.Zeng, L.Zhang, J.

(2024) Sci Adv 10: eadl4450-eadl4450

  • DOI: https://doi.org/10.1126/sciadv.adl4450
  • Primary Citation of Related Structures:  
    8U2B, 8UCR, 8UEJ

  • PubMed Abstract: 

    Caulobacter crescentus Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in Escherichia coli , maintaining infectivity against C. crescentus , which presents promising applications, including RNA delivery and phage display.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein
A [auth AA],
AA [auth BY],
AB [auth DZ],
AC [auth GA],
AD [auth IA],
AE [auth JY],
AF [auth LZ],
B [auth AB],
BA [auth CC],
BB [auth EA],
BC [auth GB],
BD [auth IB],
BE [auth KC],
BF [auth MA],
C [auth AC],
CA [auth CD],
CB [auth EE],
CC [auth GC],
CD [auth IC],
CE [auth KD],
CF [auth ME],
D [auth AG],
DA [auth CE],
DB [auth EF],
DC [auth GG],
DD [auth IG],
DE [auth KE],
DF [auth MF],
E [auth AH],
EA [auth CI],
EB [auth EG],
EC [auth GH],
ED [auth IH],
EE [auth KI],
EF [auth MG],
F [auth AI],
FA [auth CJ],
FB [auth EK],
FC [auth GI],
FD [auth II],
FE [auth KJ],
FF [auth MK],
G [auth AM],
GA [auth CK],
GB [auth EL],
GC [auth GM],
GD [auth IM],
GE [auth KK],
GF [auth ML],
H [auth AN],
HA [auth CO],
HB [auth EM],
HC [auth GN],
HD [auth IN],
HE [auth KO],
HF [auth MM],
I [auth AO],
IA [auth CP],
IB [auth EQ],
IC [auth GO],
ID [auth IO],
IE [auth KP],
IF [auth MQ],
J [auth AS],
JA [auth CQ],
JB [auth ER],
JC [auth GS],
JD [auth IS],
JE [auth KQ],
JF [auth MR],
K [auth AT],
KA [auth CU],
KB [auth ES],
KC [auth GT],
KD [auth IT],
KE [auth KU],
KF [auth MS],
L [auth AU],
LA [auth CV],
LB [auth EW],
LC [auth GU],
LD [auth IU],
LE [auth KV],
LF [auth MW],
M [auth AY],
MA [auth CW],
MB [auth EX],
MC [auth GY],
MD [auth IY],
ME [auth KW],
MF [auth MX],
N [auth AZ],
NA [auth DA],
NB [auth EY],
NC [auth GZ],
ND [auth IZ],
NE [auth LA],
NF [auth NA],
O [auth BA],
OA [auth DB],
OB [auth FC],
OC [auth HC],
OD [auth JA],
OE [auth LB],
OF [auth NB],
P [auth BE],
PA [auth DC],
PB [auth FD],
PC [auth HD],
PD [auth JE],
PE [auth LC],
PF [auth NC],
Q [auth BF],
QA [auth DG],
QB [auth FE],
QC [auth HE],
QD [auth JF],
QE [auth LG],
QF [auth NG],
R [auth BG],
RA [auth DH],
RB [auth FI],
RC [auth HI],
RD [auth JG],
RE [auth LH],
RF [auth NH],
S [auth BK],
SA [auth DI],
SB [auth FJ],
SC [auth HJ],
SD [auth JK],
SE [auth LI],
SF [auth NI],
T [auth BL],
TA [auth DM],
TB [auth FK],
TC [auth HK],
TD [auth JL],
TE [auth LM],
TF [auth NM],
U [auth BM],
UA [auth DN],
UB [auth FO],
UC [auth HO],
UD [auth JM],
UE [auth LN],
UF [auth NN],
V [auth BQ],
VA [auth DO],
VB [auth FP],
VC [auth HP],
VD [auth JQ],
VE [auth LO],
VF [auth NO],
W [auth BR],
WA [auth DS],
WB [auth FQ],
WC [auth HQ],
WD [auth JR],
WE [auth LS],
X [auth BS],
XA [auth DT],
XB [auth FU],
XC [auth HU],
XD [auth JS],
XE [auth LT],
Y [auth BW],
YA [auth DU],
YB [auth FV],
YC [auth HV],
YD [auth JW],
YE [auth LU],
Z [auth BX],
ZA [auth DY],
ZB [auth FW],
ZC [auth HW],
ZD [auth JX],
ZE [auth LY]
122Caulobacter phage phiCb5Mutation(s): 0 
UniProt
Find proteins for D7RIC2 (Caulobacter phage phiCb5)
Explore D7RIC2 
Go to UniProtKB:  D7RIC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7RIC2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Maturation proteinWF [auth M]372Caulobacter phage phiCb5Mutation(s): 0 
UniProt
Find proteins for D7RIC1 (Caulobacter phage phiCb5)
Explore D7RIC1 
Go to UniProtKB:  D7RIC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7RIC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AG [auth AB]
AH [auth BK]
AI [auth CQ]
AJ [auth EQ]
AK [auth GA]
AG [auth AB],
AH [auth BK],
AI [auth CQ],
AJ [auth EQ],
AK [auth GA],
AL [auth HO],
AM [auth IZ],
AN [auth KQ],
AO [auth ME],
BG [auth AC],
BH [auth BK],
BI [auth CU],
BJ [auth EQ],
BK [auth GB],
BL [auth HP],
BM [auth JA],
BN [auth KU],
BO [auth ME],
CG [auth AC],
CH [auth BM],
CI [auth CV],
CJ [auth ER],
CK [auth GB],
CL [auth HP],
CM [auth JA],
CN [auth KU],
CO [auth MG],
DG [auth AH],
DH [auth BQ],
DI [auth CV],
DJ [auth ER],
DK [auth GC],
DL [auth HU],
DM [auth JE],
DN [auth KU],
DO [auth MG],
EG [auth AH],
EH [auth BQ],
EI [auth CW],
EJ [auth ES],
EK [auth GC],
EL [auth HU],
EM [auth JF],
EN [auth KV],
EO [auth MK],
FG [auth AI],
FH [auth BQ],
FI [auth DB],
FJ [auth ES],
FK [auth GH],
FL [auth HU],
FM [auth JK],
FN [auth KW],
FO [auth MK],
GG [auth AI],
GH [auth BR],
GI [auth DG],
GJ [auth EW],
GK [auth GI],
GL [auth HV],
GM [auth JK],
GN [auth KW],
GO [auth MK],
HG [auth AM],
HH [auth BS],
HI [auth DG],
HJ [auth EX],
HK [auth GI],
HL [auth HW],
HM [auth JL],
HN [auth LA],
HO [auth MQ],
IG [auth AN],
IH [auth BW],
II [auth DH],
IJ [auth EX],
IK [auth GM],
IL [auth HW],
IM [auth JQ],
IN [auth LB],
IO [auth MQ],
JG [auth AN],
JH [auth BX],
JI [auth DM],
JJ [auth FC],
JK [auth GM],
JL [auth IA],
JM [auth JR],
JN [auth LG],
JO [auth MR],
KG [auth AO],
KH [auth BY],
KI [auth DN],
KJ [auth FC],
KK [auth GM],
KL [auth IB],
KM [auth JR],
KN [auth LG],
KO [auth MR],
LG [auth AO],
LH [auth BY],
LI [auth DO],
LJ [auth FD],
LK [auth GO],
LL [auth IB],
LM [auth JW],
LN [auth LH],
LO [auth MS],
MG [auth AS],
MH [auth CC],
MI [auth DO],
MJ [auth FI],
MK [auth GO],
ML [auth IC],
MM [auth JW],
MN [auth LI],
MO [auth MS],
NG [auth AT],
NH [auth CC],
NI [auth DS],
NJ [auth FJ],
NK [auth GS],
NL [auth IG],
NM [auth JX],
NN [auth LI],
NO [auth MX],
OG [auth AT],
OH [auth CD],
OI [auth DS],
OJ [auth FJ],
OK [auth GT],
OL [auth IH],
OM [auth JY],
ON [auth LI],
OO [auth NA],
PG [auth AT],
PH [auth CE],
PI [auth DT],
PJ [auth FJ],
PK [auth GY],
PL [auth II],
PM [auth JY],
PN [auth LM],
PO [auth NA],
QG [auth AU],
QH [auth CE],
QI [auth DY],
QJ [auth FK],
QK [auth HC],
QL [auth IM],
QM [auth KC],
QN [auth LM],
QO [auth NC],
RG [auth AY],
RH [auth CI],
RI [auth DY],
RJ [auth FK],
RK [auth HC],
RL [auth IM],
RM [auth KC],
RN [auth LN],
RO [auth NG],
SG [auth AY],
SH [auth CI],
SI [auth DZ],
SJ [auth FO],
SK [auth HD],
SL [auth IO],
SM [auth KC],
SN [auth LN],
SO [auth NG],
TG [auth AZ],
TH [auth CI],
TI [auth EE],
TJ [auth FO],
TK [auth HD],
TL [auth IS],
TM [auth KD],
TN [auth LO],
TO [auth NG],
UG [auth AZ],
UH [auth CK],
UI [auth EE],
UJ [auth FO],
UK [auth HE],
UL [auth IS],
UM [auth KD],
UN [auth LO],
UO [auth NI],
VG [auth AZ],
VH [auth CK],
VI [auth EF],
VJ [auth FP],
VK [auth HI],
VL [auth IS],
VM [auth KI],
VN [auth LS],
VO [auth NI],
WG [auth BA],
WH [auth CO],
WI [auth EG],
WJ [auth FU],
WK [auth HI],
WL [auth IU],
WM [auth KJ],
WN [auth LT],
WO [auth NM],
XF [auth AA],
XG [auth BE],
XH [auth CO],
XI [auth EK],
XJ [auth FU],
XK [auth HK],
XL [auth IY],
XM [auth KK],
XN [auth LU],
XO [auth NN],
YF [auth AA],
YG [auth BG],
YH [auth CO],
YI [auth EM],
YJ [auth FV],
YK [auth HO],
YL [auth IZ],
YM [auth KO],
YN [auth LY],
YO [auth NO],
ZF [auth AB],
ZG [auth BK],
ZH [auth CP],
ZI [auth EM],
ZJ [auth FW],
ZK [auth HO],
ZL [auth IZ],
ZM [auth KO],
ZN [auth LY]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1_3660:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1R01GM141659

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references