Any Unknown or Unlisted Aircraft Manufacturer
Flight Crew Air Transport Pilot (ATP)
Situational Awareness
Deviation - Altitude Crossing Restriction Not Met; Deviation - Altitude Overshoot; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy; Inflight Event / Encounter CFTT / CFIT
Flight Crew Became Reoriented
Human Factors; Aircraft
The clearance received was the EMZOH ONE RNAV WEST Transition. With approach we received the clearance for RNAV Y 28L approach; I briefed the approach. The arrival and initial portion of the approach was flown using LNAV/VNAV. The crossing altitudes were displayed in the FMS and the active altitude limitation [displayed] in magenta on the PFD. After crossing JUPAP fix above 3;700 MSL I elected to use vertical speed and increase my descent rate down to the next displayed altitude on the PFD 1;900 MSL at VODSY; I didn't realize that the intermediate fix was not loaded in the FMS thus not displayed on the PDF. I therefore crossed HEDER below the minimum on the approach plate; received a too low terrain warning and a warning from the controller to check my altitude.Cross check all fixes and altitudes on the FMS against the approach; the fix HEDER should be displayed on the FMS.
Corporate jet FO reported receiving a 'too low terrain' GPWS warning as well as a low altitude alert from ATC on approach to OAK.