I tried to figure it out myself but got stuck. It cannot symbolically represent any of the chakras now, can it?
I think perhaps you are trying too hard. As in any metaphysical question concerning the Bible, there is never one right answer. It's always about going into the meditative state that Charles Fillmore called 'the Silence,' and trusting the guidance that emerges when you focus on 'Golgotha.'
It can be helpful to go into the Silence with some background information you may have gleaned along the way. Golgotha is, we know, 'the place of the skull,' and it apparently had that name long before the events of Jesus' crucifixion. It is generally explained (in the Oxford Study Bible, for example) that the name derived from the rather skull-like shape of the hill. On a recent trip to Jerusalem, however, I found that others believe the name derives from the number of skulls that littered its surface, due to the many crucifixions.
Either or neither can be true. Or both. Metaphysically, I think you might consider the skull as an expression of our mortal selves; there is no overt spiritual connotation to the word. And it is the apparent limitations of our mortal selves that we leave behind in order to become fully our spiritual selves. That is, I think, the essence of crucifixion—we 'die' to some aspect of life that has been obstructing our true self, so that we can more forward with more freedom than ever before. And since the resistance itself is always on expression of the mind, it might be appropriate that the crucifixion experience involves the skull.