If you usually see the organization's and it's corresponding peer's will be joining a channel and do all the transactions (any operation like create,query etc ..). There is a ledger for a channel and all peer's have a copy of that ledger.
For your question
And I coudnt find when the nodes of organisations agreed to update transactions?
Let's take A as an peer from organization Org1 tries to update the value in the ledger. ( So this can be basically called as any client(application) tries to send an request to update something in ledger)
Now this request, someone has to validate. That's where endorsing peer (these are the peer's where chaincode (buisness logic) is installed) comes into picture. Now this transaction done by A will be validated by the policies that are defined in chaincode.
You can refer about endorsing peers and policies here