PfSnf2L Cryo-EM
Structure of human Snf2H on the nucleosome
PDB: SmarcA5 (5-25 15 Structures)
Cryo-EM structures of hsSNF2H (SMARCA5) - visible from aaTyr174-Ile632
downloaded mmCIF format to: 'Gernot work/Projects/Malaria/pfSNF2L/Structural analysis nuc+snf2l/hsSNF2H Cryo Structures'
visible from aaTyr174-Gln634
downloaded mmCIF format to: 'Gernot work/Projects/Malaria/pfSNF2L/Structural analysis nuc+snf2l/hsSNF2H Cryo Structures'
visible from aaTyr174-Ile632
Use these sequences to compare them to AlphaFold PfSnf2Lcore
Bacterial expression of remodeler!!!!
hsSnf2H Expressed in Bacteria: 25684208 - His-Tev-Snf2H (pET15b)
Can we express PfSnf2Lcore in bacteria? but not very active
The solved CryoEM structure of hsSNF2H is a part of PfSnf2Lcore
sequence alignement file name in geneious: PfSnf2Lcore + cryo visible of hsSNF2H
HsSnf2H Cryo-EM region: Leu106-Glu571 in PfSnf2Lcore246-843
HsSnf2H Cryo-EM region: Leu351-Glu816 in PfSnf2L (our expression clone)
AlphaFold modeling of PfSnf2Lcore (5-25):
Gernot work/Projects/Malaria/pfSNF2L/Structural analysis nuc+snf2l/PfSnf2Lcore AlphaFold 5-25
Structure of hsSNF2H to the nucleosome: 8V4Y (RCSB PDB - 8V4Y: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1))
Do the structures overlap? Yes - much similarity!
left Pf - right Hs : different charges
saved at: 'Gernot work/Projects/Malaria/pfSNF2L/Structural analysis nuc+snf2l/PfSnf2Lcore AlphaFold 5-25/PfSnf2Lcore and HsSnf2H structure comparison 5-25.pdb'
DNA-PfSnf2Lcore EMSA
15bp DNA should be enough for shift
or mimic both strands:
