Two other suspects believed to be involved in the car burglary were placed under arrest, police said.
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Police said all three suspects involved were adults.
No officers were hurt during the shooting.
It happened around 5:26 a.m. in the area of 7th and Grayson Streets while police were called to investigate an auto burglary.
Bullet holes through windows of a black SUV can be seen from the middle of the intersection where the shooting happened.
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"One of the subjects on scene was transported to highland hospital and has since succumbed to their injuries," Officer Jessica Perry, a spokesperson for the Berkeley Police Department, said. "Two other suspects on scene have been placed under arrest and were transported back to the Berkeley Police Department. None of the officers on scene were injured during this incident."
MORE: Gunman killed by police after fatally shooting employee at Toyota in Albany: authorities
Police are keeping multiple blocks shut down during the investigation.
"It's maybe two square blocks in, yeah so it's a big operation. I've never seen anything quite this big in Berkeley," Jane Anne Staw, a Berkeley resident, said.
Perry said at this point in time, it's not clear how many officers fired their weapons but every person involved was taken back to the police department for questioning and are being placed on administrative leave.
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This is the Berkeley Police Department's second deadly shooting involving an officer this year since September. The first was at the Toyota of Berkeley service center in Albany.
The homicide bureau investigators are responding to the scene as well as the district attorney's office.
People are being asked to avoid this intersection entirely here at 7th and Grayson as this area will be shut down until further notice.