SANTA CLARA — Three seasons since quarterbacking the 49ers to the NFC crown at Atlanta, Colin Kaepernick will be on the sideline when the Falcons visit the 49ers on Sunday, a change that offensive coordinator Geep Chryst traces to an overhauled roster.

“We know that the 2012 team, that he stepped in the huddle with, had a lot of really nice characteristics,” Chryst said Thursday. “Some of those elements had been put in place, in terms of the O-line, in terms of the defense, in terms of the stability he walked into.

“Here we are a couple years down the road and we still have some core elements from that 2012 team,” Chryst added, “but there’s a lot of pieces that are new.”

Besides Blaine Gabbert as their new quarterback, the 49ers could have a new starting running back in either Shaun Draughn or Pierre Thomas if Carlos Hyde remains sidelined by a foot injury. They also will have a new starting tight end after trading Vernon Davis to the Denver Broncos on Monday.

The 49ers (2-6) have the league’s least productive offense in terms of points (13.6 per game) and yards (282.3) under Chryst, their quarterbacks coach the previous four seasons.

How much is Chryst to blame for the demise of Kaepernick and the offense?

“You feel like you bear it every call that you make. You feel you bear it every practice that you do,” Chryst said. “You try to get under the hood and say, ‘OK, what is it we’re failing on?’ At the same time, as a coach, you know the hand that you’re dealt.”

General manager Trent Baalke’s roster hasn’t produced a backup lineman to supplant one of many struggling starters.

“We’ve been giving them opportunities, but they also have to seize that opportunity and base that as much on merit as just change for change’s sake,” Chryst said.

The 49ers will remain a run-based offense, Chryst said, in order to trigger play-action fakes and spark the passing game. That desire to run was never more obvious than Sunday in St. Louis, when the 49ers’ were backed up at the 3-yard line and lost a yard on three consecutive runs, resulting in a safety.

“We were having trouble blocking their front four. They’re a talented front four,” Chryst said of the Rams. “I don’t think whether you call a run or a pass, if you’re getting penetration up the middle, it really matters, because we’re getting whipped at the point of the attack.

“Whether you call something like a bomb to throw it down field or a quarterback sneak, if you’re blown up and you’re backed up, it’s not going to turn out all right. It just won’t.”

Those were the most critical comments Chryst has had all year about the offensive line’s obvious deficiencies, many of which weren’t present during the 2012 season’s Super Bowl run.

Kaepernick is expected to speak to the media Friday for the first time since getting benched Monday. Chryst wouldn’t rule out Kaepernick’s return to the starting role. “By no means, are we saying at this point moving forward, this is anything of a permanent or etched into granite nature,” Chryst said. “But where we are as an offense, we’ve got to do something, and we’ll leave no stone unturned trying to come up with a plan to win on Sunday.”

Cornerback Keith Reaser said he often has found himself helpless at defending some of Gabbert’s passes in practices. “Blaine is good. He makes some great, great throws in practice,” Reaser said. “You get angry because there’s nothing you can do about it. He’s got a quick release, a strong arm and a good understanding of coverages.” Reaser might make his first career start if Kenneth Acker is sidelined by a concussion. Acker has not practiced this week.

Left guard Alex Boone did not practice because of a knee injury, casting in doubt his availability for Sunday. Andrew Tiller could be in line to make his first career start if Boone can’t play. Boone was limited Wednesday and has been on the injury report with a knee issue since last week. He has started every game this season, as has every other offensive lineman, including left tackle Joe Staley, who participated fully Thursday despite his own knee issue.

Draughn, acquired Monday, said he’s preparing as if he’ll start Sunday, though Thomas is also trying to catch up on the 49ers’ game plan since signing Tuesday. Draughn described his running style as: “One cut, get downhill. I can make you miss or run you over. Overall, I’m decent.”

Hyde and wide receiver Anquan Boldin (hamstring) remained out of practice. Limited were tight end Garrett Celek (concussion), outside linebacker Ahmad Brooks (shoulder), safety Eric Reid (chest) and linebacker NaVorro Bowman (shoulder).