8PHU

Asymmetric structure of the portal-containing cap of the Borrelia bacteriophage BB1 procapsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Borrelia Bacteriophage phi BB1 Procapsid.

Rumnieks, J.Fuzik, T.Tars, K.

(2023) J Mol Biol 435: 168323-168323

  • DOI: https://doi.org/10.1016/j.jmb.2023.168323
  • Primary Citation of Related Structures:  
    8PHO, 8PHP, 8PHQ, 8PHR, 8PHS, 8PHT, 8PHU, 8PKH, 8QO0, 8QO1

  • PubMed Abstract: 

    Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.


  • Organizational Affiliation

    Latvian Biomedical Research and Study Center, Rātsupītes 1, 1067 Riga, Latvia. Electronic address: j.rumnieks@biomed.lu.lv.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A [auth AB],
AA [auth BD],
AB [auth CD],
AF [auth GJ],
AJ [auth KM],
AK [auth LM],
B [auth AC],
BB [auth CE],
BF [auth GK],
BG [auth HK],
BK [auth LN],
CF [auth GL],
CG [auth HL],
CH [auth IL],
DC [auth DJ],
DG [auth HM],
DH [auth IM],
DL [auth MS],
EC [auth DK],
ED [auth EK],
EH [auth IN],
EL [auth MT],
EM [auth NT],
FC [auth DL],
FD [auth EL],
FE [auth FL],
FL [auth MU],
FM [auth NU],
FN [auth OU],
G [auth AJ],
GD [auth EM],
GE [auth FM],
GI [auth JS],
GM [auth NV],
GN [auth OV],
H [auth AK],
HA [auth BK],
HE [auth FN],
HI [auth JT],
HJ [auth KT],
HN [auth OW],
I [auth AL],
IA [auth BL],
IB [auth CL],
II [auth JU],
IJ [auth KU],
IK [auth LU],
JA [auth BM],
JB [auth CM],
JF [auth GS],
JJ [auth KV],
JK [auth LV],
KB [auth CN],
KF [auth GT],
KG [auth HT],
KK [auth LW],
LF [auth GU],
LG [auth HU],
LH [auth IU],
MC [auth DS],
MG [auth HV],
MH [auth IV],
ML [auth NB],
NC [auth DT],
ND [auth ET],
NH [auth IW],
NL [auth NC],
NM [auth OC],
OC [auth DU],
OD [auth EU],
OE [auth FU],
OK [auth MB],
OL [auth ND],
OM [auth OD],
P [auth AS],
PD [auth EV],
PE [auth FV],
PI [auth KB],
PK [auth MC],
PM [auth OE],
Q [auth AT],
QA [auth BT],
QE [auth FW],
QI [auth KC],
QJ [auth LC],
R [auth AU],
RA [auth BU],
RB [auth CU],
RH [auth JB],
RI [auth KD],
RJ [auth LD],
SA [auth BV],
SB [auth CV],
SF [auth HB],
SH [auth JC],
SJ [auth LE],
TB [auth CW],
TF [auth HC],
TG [auth IC],
UE [auth GB],
UF [auth HD],
UG [auth ID],
UK [auth MJ],
VC [auth EB],
VE [auth GC],
VG [auth IE],
VK [auth MK],
VL [auth NK],
WC [auth EC],
WD [auth FC],
WK [auth ML],
WL [auth NL],
WM [auth OL],
XB [auth DB],
XC [auth ED],
XD [auth FD],
XH [auth JJ],
XL [auth NM],
XM [auth OM],
Y [auth BB],
YB [auth DC],
YD [auth FE],
YH [auth JK],
YI [auth KK],
YM [auth ON],
Z [auth BC],
ZA [auth CC],
ZH [auth JL],
ZI [auth KL],
ZJ [auth LL]
319Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: BB_L06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Decorator protein P03185Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: BB_L03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Decorator protein P05190Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: BbuZS7_P05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Scaffold protein
AG [auth HJ],
AH [auth IJ],
AL [auth MP],
AO [auth QD],
AP [auth TC],
AQ [auth UC],
AR [auth VW],
AS [auth XQ],
BC [auth DH],
BD [auth EH],
BH [auth IK],
BL [auth MQ],
BM [auth NQ],
BO [auth QE],
BP [auth TD],
BQ [auth UD],
BR [auth VX],
BS [auth XR],
CC [auth DI],
CD [auth EI],
CE [auth FI],
CL [auth MR],
CM [auth NR],
CN [auth OR],
CO [auth QF],
CP [auth TE],
CQ [auth UE],
CR [auth VY],
CS [auth XS],
DD [auth EJ],
DE [auth FJ],
DI [auth JP],
DM [auth NS],
DN [auth OS],
DO [auth QG],
DP [auth TF],
DQ [auth UF],
DR [auth VZ],
DS [auth XT],
E [auth AH],
EA [auth BH],
EE [auth FK],
EI [auth JQ],
EJ [auth KQ],
EN [auth OT],
EO [auth QH],
EP [auth TG],
EQ [auth VA],
ER [auth WA],
ES [auth XU],
F [auth AI],
FA [auth BI],
FB [auth CI],
FI [auth JR],
FJ [auth KR],
FK [auth LR],
FO [auth QI],
FP [auth TH],
FQ [auth VB],
FR [auth WB],
FS [auth XV],
GA [auth BJ],
GB [auth CJ],
GF [auth GP],
GJ [auth KS],
GK [auth LS],
GO [auth QJ],
GP [auth TI],
GQ [auth VC],
GR [auth WC],
GS [auth XW],
HB [auth CK],
HF [auth GQ],
HG [auth HQ],
HK [auth LT],
HO [auth RA],
HP [auth TJ],
HQ [auth VD],
HR [auth WD],
HS [auth XX],
IF [auth GR],
IG [auth HR],
IH [auth IR],
IN [auth OX],
IO [auth RB],
IP [auth TK],
IQ [auth VE],
IR [auth WE],
IS [auth XY],
JC [auth DP],
JG [auth HS],
JH [auth IS],
JL [auth MY],
JN [auth OY],
JO [auth SA],
JP [auth TL],
JQ [auth VF],
JR [auth WF],
JS [auth XZ],
KC [auth DQ],
KD [auth EQ],
KH [auth IT],
KL [auth MZ],
KM [auth NZ],
KN [auth OZ],
KO [auth SB],
KP [auth TM],
KQ [auth VG],
KR [auth XA],
KS [auth YA],
LC [auth DR],
LD [auth ER],
LE [auth FR],
LK [auth LX],
LL [auth NA],
LM [auth OA],
LO [auth SC],
LP [auth TN],
LQ [auth VH],
LR [auth XB],
LS [auth YB],
M [auth AP],
MD [auth ES],
ME [auth FS],
MI [auth JY],
MK [auth LY],
MM [auth OB],
MO [auth SD],
MP [auth TO],
MQ [auth VI],
MR [auth XC],
MS [auth YC],
N [auth AQ],
NA [auth BQ],
NE [auth FT],
NI [auth JZ],
NJ [auth KZ],
NK [auth LZ],
NO [auth SE],
NP [auth TP],
NQ [auth VJ],
NR [auth XD],
NS [auth YD],
O [auth AR],
OA [auth BR],
OB [auth CR],
OH [auth IX],
OI [auth KA],
OJ [auth LA],
OO [auth SF],
OP [auth TQ],
OQ [auth VK],
OR [auth XE],
OS [auth YE],
PA [auth BS],
PB [auth CS],
PF [auth GY],
PH [auth IY],
PJ [auth LB],
PO [auth SG],
PP [auth TR],
PQ [auth VL],
PR [auth XF],
PS [auth YF],
QB [auth CT],
QF [auth GZ],
QG [auth HZ],
QH [auth IZ],
QO [auth SH],
QP [auth TS],
QQ [auth VM],
QR [auth XG],
RE [auth FX],
RF [auth HA],
RG [auth IA],
RO [auth SI],
RP [auth TT],
RQ [auth VN],
RR [auth XH],
SC [auth DY],
SE [auth FY],
SG [auth IB],
SK [auth MH],
SL [auth NH],
SO [auth SJ],
SP [auth TU],
SQ [auth VO],
SR [auth XI],
TC [auth DZ],
TD [auth EZ],
TE [auth FZ],
TK [auth MI],
TL [auth NI],
TM [auth OI],
TO [auth SK],
TP [auth TV],
TQ [auth VP],
TR [auth XJ],
UB [auth CX],
UC [auth EA],
UD [auth FA],
UL [auth NJ],
UM [auth OJ],
UO [auth SL],
UP [auth TW],
UQ [auth VQ],
UR [auth XK],
V [auth AY],
VB [auth CY],
VD [auth FB],
VH [auth JH],
VI [auth KH],
VM [auth OK],
VO [auth SM],
VP [auth TX],
VQ [auth VR],
VR [auth XL],
W [auth AZ],
WA [auth BZ],
WB [auth CZ],
WH [auth JI],
WI [auth KI],
WJ [auth LI],
WO [auth SN],
WP [auth TY],
WQ [auth VS],
WR [auth XM],
X [auth BA],
XA [auth CA],
XI [auth KJ],
XJ [auth LJ],
XN [auth QA],
XO [auth SO],
XP [auth TZ],
XQ [auth VT],
XR [auth XN],
YA [auth CB],
YE [auth GH],
YF [auth HH],
YJ [auth LK],
YN [auth QB],
YO [auth TA],
YP [auth UA],
YQ [auth VU],
YR [auth XO],
ZE [auth GI],
ZF [auth HI],
ZG [auth II],
ZN [auth QC],
ZO [auth TB],
ZP [auth UB],
ZQ [auth VV],
ZR [auth XP]
230Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: BB_L02
UniProt
Find proteins for Q9R2Q2 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
Explore Q9R2Q2 
Go to UniProtKB:  Q9R2Q2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R2Q2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Decorator protein P04AI [auth JM],
DF [auth GM],
GC [auth DM],
J [auth AM],
XK [auth MM]
254Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: BB_L04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein407Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: BB_L01
UniProt
Find proteins for Q9R3K2 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
Explore Q9R3K2 
Go to UniProtKB:  Q9R3K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R3K2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONRELION3.1.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundEuropean Union1.1.1.2/VIAA/4/20/704
iNEXT-DiscoveryEuropean Union18826
iNEXT-DiscoveryEuropean Union24421

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-15
    Changes: Database references