The work, which begins Friday, is expected to take three years.
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The shuttle might only travel three blocks, but the MTA said100,000 people use it daily to get between Times Square and Grand Central.
The plan is to extend the current S train length from four cars to six cars, increasing capacity by 20%.
That will also include replacing the current signal system, which dates back to the 1930s.
The MTA will centralize the operations, meaning service will only run on one platform instead of two.
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The construction will also make the station handicap accessible, and there will be a new entrance installed as a part of the One Times Square project.
For commuters, it means waiting longer for the train during peak times.
The MTA is advising commuters to turn to the 7 train for service between the two stations.
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