Some of them use multi signature wallets to secure their funds and most of the time their overall portfolio is stored at multiple addresses. If an institution has 10k BTC they will store it in 5 or 10 different wallets. Some of the major institutions use custody services like Bitgo so that they can use insurance services as well. Some of them might keep their funds in centralized exchange to use them as leverage to use the opportunity of market manipulation by opening long and short position as most of these institutions get insider news from their sources.