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D.J. Jones signs three-year deal with Broncos [report]

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© Cary Edmondson-USA TODAY Sports

Heading into this offseason, the 49ers’ two main priorities were Laken Tomlinson and D.J. Jones. The question was whether they would retain one, let alone both.

Now we have that answer. After Tomlinson signed a reported three-year, $40 million deal with the New York Jets, D.J. Jones got his due, too.

Per Ian Rapoport of NFL Network, Jones agreed to a three-year, $30 million deal with $20 million fully guaranteed at signing.

He is essentially a one-for-one replacement for their old defensive tackle, Shelby Harris, who they shipped off to Seattle as part of the Russell Wilson trade. He was making $9 million a year and had six sacks last season.

Jones is less renowned as a pass rusher, with seven sacks over the last three seasons, but is arguably the league’s best run stopper. He led the league with a 48 percent run stop win rate last season, and was a major part of the defensive line’s resurgence down the stretch.

With both Tomlinson and Jones — not pillars, but crucial pieces of the team — gone, it begs the question as to what the 49ers plan to do with that unused money.

They are currently projected to be more than $9 million over the salary cap, but can create immediate cap room by extending Jimmie Ward or restructuring Arik Armstead or George Kittle’s contracts. They will have to get under the cap by March 16.

The big domino to fall is Jimmy Garoppolo, whose suitors have started to dry up in recent days. There is some question as to whether he may be cut outright, or how long the 49ers are willing to play hardball — likely with the Indianapolis Colts — to keep him on the roster.