[{"organizationId":339975,"domains":[{"application":"ABC","activeInd":true,"subdomain":[{"url":"URL1","clientName":"ABCClient"}]},{"application":"mno","activeInd":false,"subdomain":[{"url":"URL2","clientName":"MNOClient"}]},{"application":"pqr","activeInd":false,"subdomain":[{"url":"URL3","clientName":"pqrClient"}]},{"application":"egh","activeInd":true,"subdomain":[{"url":"URL4","clientName":"eghClient"}]}]}]

db.collection.update({"organizationId":339975},{$set:{"domains.$[elemx].subdomain.$[elemy].url":"updatedUrl3"}},{"arrayFilters":[{"elemx.application":"pqr"},{"elemy.url":"URL3"}]})