The phone call came at 4:30 in the morning on Monday.

“I have to say, it made me feel awake,” said James Rothman ’71, a biomedical sciences, cell biology and chemistry professor.

The caller wished to congratulate Rothman on his latest laurel: a Nobel Prize. Rothman, who chairs the Cell Biology department, shares the 2013 Nobel Prize in Physiology or Medicine with Randy Schekman, a professor at the University of California, Berkeley, and Thomas Südhof, a professor at Stanford University. The three will split an award of 8 million Swedish krona, or roughly $1.2 million.

The prize committee, which is based in Stockholm, cited Rothman, Schekman and Südhof for their “discoveries of machinery regulating vesicle traffic, a major transport system in our cells.”

Together, the three recipients’ research pieces together how vesicles, which are cellular cargo packages, get to where they need to go on time. Rothman’s individual contribution deals with the protein machinery that allows vesicles to dock at their destinations.

Jonathan Bogan ’86, a professor of medicine and cell biology, said that Rothman’s seminal work was completed in the late 80s and early 90s, when Rothman was teaching biochemistry at Stanford. All three of this year’s winners are affiliated with Stanford in some way — Südhof as a current professor, Rothman as a former professor and Schekman as a former doctoral student.

Bogan said many of Rothman’s colleagues were expecting him to receive the award.

“It was just a question of which year,” Bogan said.

The award cannot have come as a surprise to Rothman either. Among his previous accolades is the prestigious Lasker Award, often referred to as “America’s Nobel,” which he won in 2002. The same year, he also received the Louisa Gross Horwitz Prize. With his most recent award, Rothman has joined the 46 percent of Louisa Gross Horwitz Prize recipients who have gone on to win the Nobel.

The last time a Yale professor won a Nobel Prize was in 2009, when Thomas Steitz shared a chemistry citation “for studies of the structure and function of the ribosome.” Rothman is the fourth Yale professor to win a Nobel in Physiology or Medicine, following George Palade, another professor of cell biology, who shared the award in 1974.

Rothman said the paper that Palade co-authored inspired him to pursue his research on protein trafficking.

Cell biology professor Derek Toomre said that Rothman’s work will “open up a world of understanding membrane trafficking.”

Toomre said cells require membrane trafficking to conduct basic life processes such as transferring insulin to the pancreas. Membrane trafficking malfunctions can lead to diseases such as diabetes, he added.

“What’s really striking about Rothman is that he’s not only super intelligent, but creative and innovative as well,” Toomre said.

In 1993, Rothman discovered complexes of proteins called Soluble NSF attachment receptors, which are critical to the operation of the cellular signaling pathway. SNARE proteins recognize and “zip” onto the vesicles containing essential cellular signals and drive the vesicles to fuse with the membrane of their target location.

In his current research, Rothman employed a number of original biological tests to understand SNARE protein function. One type of in vitro test that Rothman developed allowed him to track and identify the roles of these proteins in trafficking materials through the membrane.

The Nobel Prize in Physics will be announced today.