To explain it in more detail:

1000MHz equals 1,000,000,000 Hz or clockticks per second.
This means one clocktick takes just a billionth of a second, or 1ns (nanosecond).

In case of DDR3 the CAS latency can be anywhere between 5 and 10, and determines the amount of clockticks it takes for the columnaddress-signal to complete.

Thus at 1000MHz, it takes 10ns with a CAS of 10 (10 × 1ns).
In terms of latency this is equal to CAS 5 at 500MHz (DDR2-1000), CAS 4 at 400MHz (DDR2-800), CAS 3 at 300MHz (DDR2-667), et cetera.

But the main thing people tend to forget is that, although the latency may be equal or sometimes higher, the total bandwidth is twice that of DDR2 and that's where the real benefit lies.

For example:

DDR2-1000 CAS 5
Latency: 10ns
Bandwidth: 8,000MB/s

DDR3-2000 CAS 10
Latency: 10ns
Bandwidth: 16,000MB/s

It's not all that bad.