Homology Modelling of Pacer RH domain in SWISS-MODEL

In Swiss Model,

start new modelling project

upload target sequence. Here, used the human Pacer (RUBCNL) sequence acquired from uniprot:

sp|Q9H714|PACER_HUMAN Protein associated with UVRAG as autophagy enhancer OS=Homo sapiens OX=9606 GN=RUBCNL PE=1 SV=3

MVSQSTVRQDSPVEPWEGISDHSGIIDGSPRLLNTDHPPCQLDIRLMRHKAVWINPQDVQ

QQPQDLQSQVPAAGNSGTHFVTDAASPSGPSPSCLGDSLAETTLSEDTTDSVGSASPHGS

SEKSSSFSLSSTEVHMVRPGYSHRVSLPTSPGILATSPYPETDSAFFEPSHLTSAADEGA

VQVSRRTISSNSFSPEVFVLPVDVEKENAHFYVADMIISAMEKMKCNILSQQQTESWSKE

VSGLLGSDQPDSEMTFDTNIKQESGSSTSSYSGYEGCAVLQVSPVTETRTYHDVKEICKC

DVDEFVILELGDFNDITETCSCSCSSSKSVTYEPDFNSAELLAKELYRVFQKCWILSVVN

SQLAGSLSAAGSIVVNEECVRKDFESSMNVVQEIKFKSRIRGTEDWAPPRFQIIFNIHPP

LKRDLVVAAQNFFCAGCGTPVEPKFVKRLRYCEYLGKYFCDCCHSYAESCIPARILMMWD

FKKYYVSNFSKQLLDSIWHQPIFNLLSIGQSLYAKAKELDRVKEIQEQLFHIKKLLKTCR

FANSALKEFEQVPGHLTDELHLFSLEDLVRIKKGLLAPLLKDILKASLAHVAGCELCQGK

GFICEFCQNTTVIFPFQTATCRRCSACRACFHKQCFQSSECPRCARITARRKLLESVASA

AT

Search for template

Search should yield a top hit corresponding to the Alphafold model of Pacer, and subsequent hits represent using the Rubicon RH domain as a template (6wcw).

Select the hit that aligns Pacer to the Rubicon structure (6wcw), and > build model. From here, the file can be downloaded as a PDB and used in downstream modelling steps.

Open Pymol

open downloaded Pacer homology model

fetch rubicon-rab7 dimer crystal structure by typing "fetch 6wcw" in the command line

Align Rubicon crystal structure and Pacer homology model using the "align" command.

Delete rubicon monomer, and expansion binding site between the pacer homology model and rab7. Focus on S72 of Rab7