49ers’ Kyle Shanahan-Steve Wilks dynamic is extremely tense right now

For most of Kyle Shanahan’s stint as 49ers head coach, he’s mostly stuck to running the red and gold offense and entrusted the defense to his defensive coordinator.

He seems ready to change that this week.

Speaking to reporters Wednesday, Shanahan offered some fiery comments about DC Steve Wilks’ controversial blitz call in the first half of San Francisco’s Monday Night Football match-up against the Vikings. With 16 seconds left in the half, Wilks called for seven people to blitz Vikings quarterback Kirk Cousins, leaving no safety help to stop Vikings wide receiver Jordan Addison once the rookie wrestled a pass away from 49ers cornerback Charvarius Ward. Addison ran straight into the end zone for a 60-yard touchdown.

“I have no problem with zero blitzes, especially when people need a lot of yards,” Shanahan said. “If you need to get 20 yards to kick a field goal, I have no problem with a zero blitz. But I do when there’s 16 seconds left. That’s where he lost track. There was no necessary need for that just because of the time. … I have no problem with that play call, but when it’s that time, you can’t do that. That’s not an option.”

There’s also star defensive end Nick Bosa’s remark about things being “a little different this year” with regard to the pass-rush strategy. Combine that with Shanahan’s comments and there are questions about how Wilks is adjusting to the 49ers. Wilks was brought in this offseason after finishing last year as interim head coach of the Carolina Panthers to be a veteran presence and keep things rolling for one of the NFL’s best defenses, but things have been rocky on that side of the ball of late.

To his credit, Wilks opened his weekly press conference Thursday by owning his decision. “I take full responsibility for that call,” he said. “I have to do a better job in putting the guys in a better position. We have good players. I know that and can’t really press the issue and with that moving forward, it’s my responsibility to do that. So I wish I could take it back, but again, I’ve got to do better.”

Of course, Shanahan could’ve overruled the playcall or called a timeout as head coach. On his weekly radio hit with KNBR’s “Tolbert and Copes” show, after Wilks’ press conference, he acknowledged his own role in the play.

“Ultimately, it’s up to me,” Shanahan said Thursday. “I heard that and I should have called timeout and changed it. But I didn’t, so that’s what happened.”

Under Shanahan, defensive coordinators typically get a wide berth to run that side of the ball —  and can shine. Both Robert Saleh and DeMeco Ryans took starring turns as the 49ers’ DC and landed head coaching jobs afterward, with Ryans leaving for the Texans last offseason.

The 49ers brass is saying all of the right things about the relationship between Shanahan and Wilks, with general manager John Lynch telling KNBR’s “Murph and Mac” morning show Friday that the team is “squarely behind Steve Wilks.” But Wilks is a longtime defensive coach, and the mandate that he adjust to the 49ers’ system rather than having the team adjust to him seems to be taking a toll.

“You know it’s always challenging,” Wilks said Thursday. “When you’ve done your own thing for 17 years, it’s a little different, but I’m encouraged. I got a great supporting cast. These coaches around me are phenomenal. They know this defense. They know their craft. These players are great. So we’re all in this together, man. So I’m not hitting the panic button at all.”