SANTA CLARA, Calif. >> Nick Bosa’s lengthy contract holdout ended four days before the start of the season for the San Francisco 49ers when he agreed to a contract extension that will make him the NFL’s richest defensive player ever.

Coach Kyle Shanahan said today that the two sides agreed to the contract and that Bosa is on his way to the team facility. Now Shanahan is glad he can stop thinking about what it would be like for the Niners to open their season without their best defensive player.

“You try not to think about it much because it’s not really in my control and let the process play itself out,” Shanahan said. “As it went through the weekend, I just kind of got it in my mind that we weren’t playing with him. If I had gone back and forth, I would have been miserable. I just decided we weren’t. … It’s a hell of a bonus to get him here. We’re obviously really excited about it.”

Shanahan said Bosa would have to show up with a “beer belly” and “be out of shape” not to play the season opener at Pittsburgh on Sunday but added that’s “not in Bosa’s DNA.”

How much he is able to play after spending all of training camp working out on his own remains to be seen.

“We’ll see when he gets here,” Shanahan said. “I know Nick will come in shape. I know he’ll be good. … We’ll be smart with it and that will be based on these next two practices.”

But getting the deal done in time for Bosa to play this week provides a big boost for a team that comes into the season with championship aspirations and doesn’t need to contemplate the worst-case scenario with Bosa.

The news came shortly before the Niners took the field for practice today, with many of his teammates finding out when linebacker Fred Warner ran through the locker room screaming about the news as the cloud of the holdout had been lifted.

“I’d be lying to say it wasn’t (a cloud) because he’s such a huge contributor to what we do as a defense and how we play,” All-Pro left tackle Trent Williams said. “It’s not like anybody else is going down. The Defensive Player of the Year. You miss players like that. I know it’s a “next man up league” but a lot of that goes out the window when you’re talking about a player like Nick.”

The 49ers have had a strong history of rewarding their own stars, giving big extensions the past three summers to tight end George Kittle, Warner and receiver Deebo Samuel. But getting a deal done with Bosa proved to be more complicated.

ESPN first reported the extension and said it was worth $170 million over five seasons with $122.5 million guaranteed. The average annual payout of $34 million tops the previous mark of $31.7 million for Rams defensive tackle Aaron Donald and the guarantees top the $102 million Bosa’s older brother, Joey, got from the Chargers in 2020.

“I thought it would come to fruition sometime last week, and it didn’t,” Shanahan said. “It made me nervous, made me kind of move on with it. But we all knew Nick would get rewarded like he did.”

Bosa earned the lucrative new deal with stellar play since being drafted second overall in 2019. He was the AP Defensive Rookie of the Year and was voted the top defensive player in the NFL last season when he led the league with 18 1/2 sacks.

Bosa has 34 sacks the past two seasons after having nine as a rookie in 2019. He had no sacks in two games in 2020 when he went down with a season-ending knee injury.

In Bosa’s three healthy seasons, San Francisco ranks third in points allowed, second in yards per play allowed, fourth in sacks and tied for sixth in takeaways.

“I’m sure everybody knows how he makes everybody’s life easier, not just me, being one of the most dominant defensive players in the league, in the run and pass game,” Warner said. “He’s the most complete player on the edge. That clears a lot of things up for me.”

NOTES: The Niners selected six captains for the season: Williams, Warner, QB Brock Purdy, WR Deebo Samuel, TE George Kittle and DL Arik Armstead. … Returner/WR Ray-Ray McCloud (wrist) and K Jake Moody (quadriceps) returned to practice and were limited. … LB Oren Burks (knee), S Tashaun Gipson (back), S Talanoa Hufanga (knee), Kittle (groin) and RB Jordan Mason (foot) were also limited. … Backup OL Jon Feliciano (illness) missed practice.