| acceptable | BPP22:EXLYS | 2016-05-03 19:34:03 CDT | GO:0098015 virus tail (C) | PMID:16970964 | ECO:0000314 direct assay evidence used in manual assertion | Figure 9. Negative stain electron microscopy of tail accessory factor gp4 bound to P22 portal protein rings. (a)
Negative stain electron microscopy image of purified P22 portal protein rings. Many “donut-like” structures are
visible, which in most (rarer) side view cases adopt a head-to-head conformation. (b) Negative stain micrograph of gel
filtration purified portal protein in complex with gp4.
Micrographs of the gp1:gp4
complex were compared to gp4-free portal rings, as
shown in Figure 9(a) and (b), respectively. The
majority of gp1:gp4 complexes seen on the micrographs
displayed a preferential orientation on the
grid with the central hole perpendicular to the grid.
In rare instances single complexes and head-tohead
dimers of the gp1:gp4 complex were seen in
side view (see higher magnifications in Figure 9(b))
| challenge |
| unacceptable | BPP22:EXLYS | 2016-05-03 19:34:04 CDT | GO:0046798 viral portal complex (C) | PMID:16970964 | ECO:0000314 direct assay evidence used in manual assertion | Figure 7. Isolating the gp1:gp4 assembly intermediate on agarose gel. (a) Native agarose gel run at 30 °C showing a
stably populated gp(1)12:gp(4)6 assembly intermediate. In lane 1 is dodecameric portal protein gp(1)12. The gp(1)12:gp(4)6
assembly intermediate in lanes 2 and 3 migrates on gel as a slightly lower mobility band, clearly distinguishable from fully
saturated decorated gp(1)12:gp(4)12 complex in lane 4 and free dodecameric portal protein gp(1)12 in lane 4. The
intermediates in lanes 2 and 3 were formed by adding six equivalents of gp4 to gp(1)12 and incubating the complex at 30 °C
for 30 s and 30 min, respectively. In lane 4 approximately eight equivalents of gp4 were added, yielding the fully decorated
gp(1)12:gp(4)12 complex and free gp(1)12. (b) Titration of gp4 binding to gp1 at 30 °C. By running the agarose gel at 30 °C
both gp(1)12:gp(4)6 assembly intermediate and fully decorated gp(1)12:gp(4)12 portal protein are visible on the same
titration. The assembly intermediate appears at stoichiometries gp(1):gp(4) equal to 12 (lanes 3−6) and fades away in lane 7,
where >six equivalents of gp4 are present.
Micrographs of the gp1:gp4
complex were compared to gp4-free portal rings, as
shown in Figure 9(a) and (b), respectively. The
majority of gp1:gp4 complexes seen on the micrographs
displayed a preferential orientation on the
grid with the central hole perpendicular to the grid.
In rare instances single complexes and head-tohead
dimers of the gp1:gp4 complex were seen in
side view (see higher magnifications in Figure 9(b)).
Such side views are particularly informative, in that
the dodecameric portal protein without bound gp4
forms a mushroom-shaped structure with a channel
through the center
| challenge |
| unacceptable | BPP22:EXLYS | 2016-05-03 19:57:37 CDT | GO:0019073 viral DNA genome packaging (P) | PMID:6363718 | ECO:0000315 mutant phenotype evidence used in manual assertion | Fro. I. Dependenc~ of phage formation in vitro on the concentration of the capsid donor extract.
Infected ¢~zl[ extracts containing incomplete capsids were freshly thawed and lysed as described in
Materials and Methods. D~uted .samples were mixed with concentrated protein donor extract {5-) and
incubated for I h at 23°C, at which time the reactions were stopped by further dilution and titered for
viable phage. The background of the protein donor extract was 102 phage/mi. The background of the
• at mo.~l, Conc-entrated calmid donor extracts were (0) 3.3× 10 (4- extract), (t) 2:5 × l0 T (10- extract)
and (at) 2 x 103 (26-extract).
Fro. 4. Dependence of in vitro a.~.~em!~ly on the concentration of the 4", lO ÷ and 26* activities. (a)
Com|)lementation of 10- extracts (O), 26- extracts (11) and 4- extracts (~lk) with protein donor
extract. The cap,aid extracts were diluted 25-fold, to a final infected cell cont'entration of about
2 x 10 ° c~lls/ml. Samples were mixed with serial dilutions of the 5- prc)tein donor. The maximum
slo|~s determined from these curve,a were: 4+ activity, 5 to 6; 26 + activity. I to 2; 10 + activity, 4 to 5.
The background of the undiluted extracts were protein donor 10a; 4- extract < 10s; 10- extracts,
5 x 10~; 26- extract, 2 x l0 a. (b) Variation of the ratio of cap`aid,a to protein; complemcntation of 4-
~'apsids with cap,aid donor cell concentration: (O) 5x lO 9 cell,a/ml; (A) 2 x l0 s cell,a/ml; (m) 4 x i0 v
(~lls/ml. The protein donor extract was from the same batch a.s used in (a).
| challenge |
| unacceptable | BPP22:VG10 | 2016-05-03 20:07:07 CDT | GO:0019073 viral DNA genome packaging (P) | PMID:6363718 | ECO:0000315 mutant phenotype evidence used in manual assertion | Fro. 4. Dependence of in vitro a.~.~em!~ly on the concentration of the 4", lO ÷ and 26* activities. (a)
Com|)lementation of 10- extracts (O), 26- extracts (11) and 4- extracts (~lk) with protein donor
extract. The cap,aid extracts were diluted 25-fold, to a final infected cell cont'entration of about
2 x 10 ° c~lls/ml. Samples were mixed with serial dilutions of the 5- prc)tein donor. The maximum
slo|~s determined from these curve,a were: 4+ activity, 5 to 6; 26 + activity. I to 2; 10 + activity, 4 to 5.
The background of the undiluted extracts were protein donor 10a; 4- extract < 10s; 10- extracts,
5 x 10~; 26- extract, 2 x l0 a. (b) Variation of the ratio of cap`aid,a to protein; complemcntation of 4-
~'apsids with cap,aid donor cell concentration: (O) 5x lO 9 cell,a/ml; (A) 2 x l0 s cell,a/ml; (m) 4 x i0 v
(~lls/ml. The protein donor extract was from the same batch a.s used in (a).
ependenc~ of phage formation in vitro on the concentration of the capsid donor extract.
Infected ¢~zl[ extracts containing incomplete capsids were freshly thawed and lysed as described in
Materials and Methods. D~uted .samples were mixed with concentrated protein donor extract {5-) and
incubated for I h at 23°C, at which time the reactions were stopped by further dilution and titered for
viable phage. The background of the protein donor extract was 102 phage/mi. The background of the
• at mo.~l, Conc-entrated calmid donor extracts were (0) 3.3× 10 (4- extract), (t) 2:5 × l0 T (10- extract)
and (at) 2 x 103 (26-extract).
| challenge |
| unacceptable | BPP22:NEEDL | 2016-05-03 20:11:28 CDT | GO:0019073 viral DNA genome packaging (P) | PMID:6363718 | ECO:0000315 mutant phenotype evidence used in manual assertion | Fro. I. Dependence of phage formation in vitro on the concentration of the capsid donor extract.
Infected cell[ extracts containing incomplete capsids were freshly thawed and lysed as described in
Materials and Methods. Diluted .samples were mixed with concentrated protein donor extract {5-) and
incubated for I h at 23°C, at which time the reactions were stopped by further dilution and titered for
viable phage. The background of the protein donor extract was 102 phage/mi. The background of the
• at mo.~l, Conc-entrated calmid donor extracts were (0) 3.3× 10 (4- extract), (t) 2:5 × l0 T (10- extract)
and (at) 2 x 103 (26-extract).
Dependence of in vitro assembly on the concentration of the 4", lO ÷ and 26* activities. (a)
Complementation of 10- extracts (O), 26- extracts (11) and 4- extracts (~lk) with protein donor
extract. The capsid extracts were diluted 25-fold, to a final infected cell conventration of about
2 x 10 ° c~lls/ml. Samples were mixed with serial dilutions of the 5- protein donor. The maximum
slo|~s determined from these curve,a were: 4+ activity, 5 to 6; 26 + activity. I to 2; 10 + activity, 4 to 5.
The background of the undiluted extracts were protein donor 10a; 4- extract < 10s; 10- extracts,
5 x 10~; 26- extract, 2 x l0 a. (b) Variation of the ratio of cap`aid,a to protein; complemcntation of 4-
capsids with cap,aid donor cell concentration: (O) 5x lO 9 cell,a/ml; (A) 2 x l0 s cell,a/ml; (m) 4 x 10 v
(~lls/ml. The protein donor extract was from the same batch a.s used in (a).
| challenge |
| unacceptable | BPP22:EXLYS | 2016-05-03 20:20:39 CDT | GO:0019073 viral DNA genome packaging (P) | PMID:21439834 | ECO:0000314 direct assay evidence used in manual assertion | Comparing the portal position in the procapsid and the virion shows that the portal increases its contact with the capsid shell during maturation (Figure S1). We propose that this portion of the scaffold remains in place during dsDNA packaging, allowing access of the gp4 C terminus to the bottom of the portal. When gp4 binds, the scaffold protein is displaced allowing the final conformational change implied by the position of the gp4-C-terminal polypeptide that is wedged between the capsid and portal.
| challenge |
| updatedbyinstructor | BPP22:PORTL | 2016-05-03 20:31:11 CDT | GO:0098006 viral DNA genome packaging, headful (P) | PMID:1569567 | ECO:0000315 mutant phenotype evidence used in manual assertion | | challenge |
