Motherboard connectors pinouts
USB 3.0 contains normal USB 2.0 connections. This is commonly for PC cases that have ports that don't match the Available headers. Converting from 3.0 -> 2.0 is flawless, but converting from 2.0 -> 3.0 will make your 3.0 ports active, but will only function at 2.0 speeds.

USB 3.0 Header is a 20 pin 2mm pitch header using the less common ICC pin numbering. The header has a key slot on the pin 1-10 side if enclosed.

USB 2.0 Header is a 10 pin .1 pitch header using the standard IDC pin numbering. The header has a key slot on the pin 1-9 side if enclosed. (The 10-pin IDC male graphic shown has the keying on the wrong side).

Both headers contain two ports each, and have a missing pin for filled female connectors.

USB 3.0   USB 2.0

Pin
Number

(ICC)

Equivelent

IDC Pin #

Pin
Name
Description Port Pin
Name

Pin
Number

(IDC)

1 1 VBus +5V Power 1 +5V 1
2 3 SSRX1- SuperSpeed recevier
3 5 SSRX1+
4 7 GND Ground for Power GND 7
5 9 SSTX1- SuperSpeed transmitter
6 11 SSTX1+
7 13 DRAIN Ground for Shield Drain Shared pin 10
8 15 D1-  USB 2.0 data D1- 3
9 17 D1+ D1+ 5
10 19 NC    
11 20 D2+  USB 2.0 data 2 D2+ 6
12 18 D2- D2- 4
13 16 DRAIN Ground for Shield Drain S-GND 10
14 14 SSTX2+ SuperSpeed transmitter
15 12 SSTX2-
16 10 GND Ground for Power GND 8
17 8 SSRX2+ SuperSpeed recevier
18 6 SSRX2-
19 4 VBUS +5V Power +5V 2
20 2 No Pin Space of Filled Keying   No Pin 9

 

The standard USB 2.0 Header is missing pin 9 (for keying), but logically pin 9 is for port1's Sheild GND. The sheild is left unconnected if a single port cable is plugged in to port 1. Dual Port hear connectors, share port 10 for both sheilds

This is the most common USB 2.0 header (10 pin [2x5], missing pin 9)  and it is pin compatable with the rare 8 pin [2x4] version (missing pins 9 and 10) and 10 pin [2x5] (no pins missing). It is not pin compatable with the very rare (10 pin [2x5], missing pins 10 and 2).

A new feature of USB 3.0 is the SuperSpeed bus, which provides a fourth transfer mode at 5.0 Gbit/s, this is simply left out of the 2.0 header.

 

20 pin ICC female connector layout
20 pin ICC female connector
at the 3.0 end
10 pin IDC keyed male connector layout
10 pin IDC keyed male connector
at the 1.0/1.1/2.0 end
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USB 3.0 Header to USB 2.0 Header visual pinout:
USB 3.0 Header to USB 2.0 Header diagram
click to enlarge
Source(s) of this and additional information: http://www.frontx.com/cpx101_2.html, Gigbyte MB manual GA-Z77-D3H,http://www.overclock.net/t/1241498/usb-3-0-20pin-motherboard-header-can-it-be-split-into-2
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