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Cacao

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GO:0039622T=16 icosahedral viral capsidPMID:12574112ISM: Inferred from Sequence Model PMID:10797014 C
This annotation made on page: HHV11:MCP
By: Rayesd (group Team Kendrick Jafars) on 2016-04-25 12:01:02 CDT.




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Entry TypeChallenging User,GroupTime/DateChallenge ReasonPoints/Assessment
Private
Assessment		Suzialeksander2016-05-27 12:07:07 CDTYou need to be an instructor to view these notes.Unacceptable
✗ Evidence
✗ Unique/Original
Public
Assessment		DanielRenfro2016-05-04 17:51:16 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0039622 T=16 icosahedral viral capsid PMID:12574112 IDA: Inferred from Direct Assay C The authors isolate a 65kda fragment of VP5 by "limited trypsin digestion." They then identifiy this fragment as the upper domain of VP5 by x-ray crystallography. Fig 1. shows this crystalized structure of the upper domain. It identifies areas important for both interactions between VP5 proteins and interactions with other capsid proteins like VP26. The authors also identify a novel fold that is unique to the herpesvirus. complete
CACAO 11929
on HHV11:MCP
Flagged
Public
Assessment		DanielRenfro2016-04-30 14:19:55 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0039622 T=16 icosahedral viral capsid PMID:12574112 IDA: Inferred from Direct Assay C The authors isolate a 65kda fragment of VP5 by "limited trypsin digestion." They then identifiy this fragment as the upper domain of VP5 by x-ray crystallography. Fig 1. shows this crystalized structure and identifies a novel fold that is unique to the herpesvirus Fig. 2 provides more evidence of the identity of VP5 as the major capsid protein through cryoelectron microscopy. It puts VP5 into context by depicting its placement in the entire viral capsid. The cryoelectron microscopy map of the HSV-1 capsid was obtained from a publication by Zhou et al (PMID:10797014). complete
CACAO 11929
on HHV11:MCP
Flagged
Public
Assessment		AAJohnson2016-04-29 13:44:58 CDT

Protein sequence in the publication and the uniprot ID are the same- the student go the uniprot id from the PDB page.

Requires Changes
✔ Protein
Public
Assessment		AAJohnson2016-04-29 10:52:15 CDT

I think you have two separate annotations here, though I really like how you connected the two figures. Perhaps this is really IDA, and not ISM, with just using Figure 2 to support the crystallization results in Figure 1.

Figure 1 shows the part they crystallized. If it conforms with typical capsid fold, I believe you should use IDA. Crystallization is an experiment.

Figure 2 - Find the publication for the tool used - Foldhunter, and perhaps also Molecular Modeling Toolkit, see their methods description.

I would like to verify the capsid protein you are annotating is the same protein they crystallized, and there are no strain variations in sequence.

Requires Changes
✔ Evidence
✗ With/From


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