A years-long US government probe of Binance Holdings Ltd. came to an end on Tuesday when the world’s largest crypto exchange agreed to pay a $4.3 billion fine, while the company and its former chief executive officer, Changpeng Zhao, agreed to plead guilty to criminal charges.

Under a sweeping deal worked out with the government and designed to keep the company operating, Zhao will also pay a $50 million fine and stepped down as head of the company. Binance was charged with three counts, including money laundering violations, conspiracy to conduct an unlicensed money transmitting business in the US, and sanctions …