Multiple Spanning Tree uses a special instance called the Internal Spanning Tree which runs on the first instance with the instance number of 0. A typical Cisco round can support up to 16 MSTs. MSTs 1 to 15 can be assigned to specific VLANs.
This special instance runs on all switch port interfaces in the Multiple Spanning Tree region regardless of what VLANs are associated with the ports.
In the BPDUs that the Internal Spanning Tree that it distributes are additional information regarding other Multiple Spanning Tree Instances (MSTIs). By keeping this information in the special instance it minimises the number of BPDUs that need to be transferred whilst still providing the compulsory information to calculate the spanning tree protocol factors.