The protocol keeps record of the transaction fees for the tier 1 transactions in block headers with the key 'feePerTx'.
In the screenshot below showing details of a block (block number 3,794,620 on testnet) you can see the transaction fees as well that is applicable to the tier 1 transactions (transaction requiring max of 12,000,000 gas). If a transaction falls in any other subsequent tier, then the protocol uses the same transaction fees value and a multiplying factor applicable to the subject tier to know the gas price for the subject transaction. For example for a tier 2 transaction it will be multiplied by 1500 (that is 0.0005 * 1500 = 0.75$ in terms of USD value)
In the screenshot below you can see the exact same fees being charged to a transaction that falls under tier 1. This is is one of the transactions in the same block for which details are shown above.
