Residue numbering

While figuring out the (easy) numbering scheme, having the GpHR Alignment in another window will be very helpful!

The transmembrane region

Let's start off with the already described part of GPCR numbering.
While we would love to have only one numbering scheme for the easy identification of conserved residues, a number of numbering systems for GPCRs have been suggested and used.
The GPCRDB numbering (or Oliveira numbering) and Ballesteros numbering are the most useful, but each of them still has its anomalies. Instead of giving the same decimal number to the most conserved residue in each TM, we see that for the leucine in TM2, the GPCRDB number is 220, but for the arginine in TM3 it is 340. Ideal would have been 250 and 350.
The Ballesteros numbering is more straightforward and uses indeed the "50" decimal to pinpoint the most conserved residue. Too bad they made a miscalculation in the conservation of residues. According to them D2.50 and P5.50 are the most conserved residues in TMs 2 and 5, but taking all GPCR sequences into consideration (and calculated with the Alignment Explorer), the most conserved residue in TM2 is the Leucine (2.46) (as in the GPCRDB scheme) and the one in TM5 is the Tyrosine (5.58).

Both numbering schemes have been implemented in the GlycoProtein Hormone Receptor Mutation Database (GPMD), so you can use the scheme you feel most comfortable with.

Below is a table for the interconversion between the Ballesteros and the GPCRDB numbering, using the sequence of the Human TSHR as example. Because it seems clear that also Helix 8 is conserved in the Class A GPCRs, we have introduced a numbering for the loop between helix 7 and 8 (has the same length in all Class A GPCRs) and for Helix 8. The numbering is an extension to the Ballesteros numbering (I call it Ballesteros-Extended) and starts right after 7.54 with 8.45 and we annotated the conserved phenylalanine in Helix 8 as 850.

TM 1
Residue M G Y K F L R I V V W F V S L L A L L G N V F V L L I L L T	Ballesteros 1.30 1.31 1.32 1.33 1.34 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45 1.46 1.47 1.48 1.49 1.50 1.51 1.52 1.53 1.54 1.55 1.56 1.57 1.58 1.59	GPCRDB 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139

TM 2
Residue V P R F L M C N L A F A D F C M G M Y L L L I A S V D L Y T	Ballesteros 2.38 2.39 2.40 2.41 2.42 2.43 2.44 2.45 2.46 2.47 2.48 2.49 2.50 2.51 2.52 2.53 2.54 2.55 2.56 2.57 2.58 2.59 2.60 2.61 2.62 2.63 2.64 2.65 2.66 2.67	GPCRDB 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241

TM 3
Residue G P G C N T A G F F T V F A S E L S V Y T L T V I T L E R W Y A I	Ballesteros 3.22 3.23 3.24 3.25 3.26 3.27 3.28 3.29 3.30 3.31 3.32 3.33 3.34 3.35 3.36 3.37 3.38 3.39 3.40 3.41 3.42 3.43 3.44 3.45 3.46 3.47 3.48 3.49 3.50 3.51 3.52 3.53 3.54	GPCRDB 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344

TM 4
Residue R H A C A I M V G G W V C C F L L A L L P L V	Ballesteros 4.40 4.41 4.42 4.43 4.44 4.45 4.46 4.47 4.48 4.49 4.50 4.51 4.52 4.53 4.54 4.55 4.56 4.57 4.58 4.59 4.60 4.61 4.62	GPCRDB 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432

TM 5
Residue L A L A Y I V F V L T L N I V A F V I V C C C Y V K	Ballesteros 5.35 5.36 5.37 5.38 5.39 5.40 5.41 5.42 5.43 5.44 5.45 5.46 5.47 5.48 5.49 5.50 5.51 5.52 5.53 5.54 5.55 5.56 5.57 5.58 5.59 5.60	GPCRDB 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530

TM 6
Residue D T K I A K R M A V L I F T D F I C M A P I S F Y A L S A I L	Ballesteros 6.30 6.31 6.32 6.33 6.34 6.35 6.36 6.37 6.38 6.39 6.40 6.41 6.42 6.43 6.44 6.45 6.46 6.47 6.48 6.49 6.50 6.51 6.52 6.53 6.54 6.55 6.56 6.57 6.58 6.59 6.60	GPCRDB 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630

TM 7 - Helix 8
Residue N S K I L L V L F Y P L N S C A N P F L Y A I F T K A F Q R D V F I L L S K	Ballesteros+Helix8 7.33 7.34 7.35 7.36 7.37 7.38 7.39 7.40 7.41 7.42 7.43 7.44 7.45 7.46 7.47 7.48 7.49 7.50 7.51 7.52 7.53 7.54 7.55 7.56 8.47 8.48 8.49 8.50 8.51 8.52 8.53 8.54 8.55 8.56 8.57 8.58 8.59 8.60	GPCRDB 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 807 808 809 810 811 812 813 814 815 816 817 818 819 820

The intra- and extracellular loops

All GpHRs have an equal number of residues in the loop regions between the transmembrane helices. We have therefore decided to number the loop residues. The numbering of the first loop residue begins with an 'L' (indicating Loop), followed by the number of the TM before the loop, followed by the first 10th decimal. From there on we number downstream. Applying this numbering scheme (using hTSHR as example) makes it possible to query the database for any loop residue among the three receptor classes:

Loop1-2
Residue S H Y K L N	Number L110 L111 L112 L113 L114 L115

Loop2-3
Residue H S E Y Y N H A I D W Q T	Number L210 L211 L212 L213 L214 L215 L216 L217 L218 L219 L220 L221 L222

Loop3-4
Residue T F A M R L D R K I R L	Number L310 L311 L312 L313 L314 L315 L316 L317 L318 L319 L320 L321

Loop4-5
Residue G I S S Y A K V S I C L P M D T E T P	Number L410 L411 L412 L413 L414 L415 L416 L417 L418 L419 L420 L421 L422 L423 L424 L425 L426 L427 L428

Loop5-6
Residue I Y I T V R N P Q Y N P G D K	Number L510 L511 L512 L513 L514 L515 L516 L517 L518 L519 L520 L521 L522 L523 L524

Loop6-7
Residue N K P L I T V S	Number L610 L611 L612 L613 L614 L615 L616 L617

The extracellular domain (ECD)

To allow easy and consequent searching throughout the GPMD and furthermore to facilitate the communication between researchers of different GpHRs, we have introduced a general numbering scheme for the ECD of the three major classes of GpHRs (TSHR, FSHR, LHR). Such a numbering scheme can only be introduced when the ECDs of all these receptors are perfectly alignable, and as we know, they all are.

Smits et al have described in their EMBO paper a canonical LRR motif : X1 X2 L X3 L X4 X5
X3 is a hydrophylic residue sticking out into the center of the horseshoe shaped ECD and lies between the two hydrophobic residues (L, I, V), which confine the Leucine-rich repeat structure. The picture below was taken from the paper and annotates these residues in the hTSHR, hLH/CGr and hFSHR.

Of course, we cannot use this limited numbering scheme with X's and L's, but we have decided to assign the numbers 1050, 2050, 3050, 4050, 5050, 6050, 7050, 8050 and 9050 to the X3 residue in the LRR1, LRR2, LRR3, LRR4, LRR5, LRR6, LRR7, LRR8 and LRR9, respectively.
These residues in the hTSHR are indicated in blue in the picture below (don't mind 4050, it's a little glycine):

Picture made with YASARA (http://www.yasara.org)

We consider a Leucine Rich Repeat as a beta strand followed by a coil, a helical region and again a small coil: Strand-Coil-Helix-Coil
We begin the numbering of each LRR just before the strand starts. The first residue of each LRR is indicated in the picture below in purple.
First we assign the 1050, 2050, etc to the X3 residue and from there we number upstream and downstream until the next or previous LRR.

Picture made with YASARA (http://www.yasara.org)

And here at last, the complete numbering of the ECD, using hTSHR as an example:

LRR 1
Residue T Q T L K L I E T H L R T I P S H A F S N L P N	Number 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069

LRR 2
Residue I S R I Y V S I D V T L Q Q L E S H S F Y N L S K	Number 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070

LRR 3
Residue V T H I E I R N T R N L T Y I D P D A L K E L P	Number 3046 3047 3048 3049 3050 3051 3052 3053 3054 3055 3056 3057 3058 3059 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069

LRR 4
Residue L L K F L G I F N T G L K M F P D L T K V Y S T D I	Number 4045 4046 4047 4048 4049 4050 4051 4052 4053 4054 4055 4056 4057 4058 4059 4060 4061 4062 4063 4064 4065 4066 4067 4068 4069 4070

LRR 5
Residue F F I L E I T D N P Y M T S I P V N A F Q G L C N	Number 5046 5047 5048 5049 5050 5051 5052 5053 5054 5055 5056 5057 5058 5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5070

LRR 6
Residue E T L T L K L Y N N G F T S V Q G Y A F N G T	Number 6045 6046 6047 6048 6049 6050 6051 6052 6053 6054 6055 6056 6057 6058 6059 6060 6061 6062 6063 6064 6065 6066 6067

LRR 7
Residue K L D A V Y L N K N K Y L T V I D K D A F G G V Y S	Number 7045 7046 7047 7048 7049 7050 7051 7052 7053 7054 7055 7056 7057 7058 7059 7060 7061 7062 7063 7064 7065 7066 7067 7068 7069 7070

LRR 8
Residue G P S L L D V S Q T S V T A L P S K G L E	Number 8045 8046 8047 8048 8049 8050 8051 8052 8053 8054 8055 8056 8057 8058 8059 8060 8061 8062 8063 8064 8065

LRR 9
Residue H L K E L I A R N T W T L K K L P L S L S	Number 9045 9046 9047 9048 9049 9050 9051 9052 9053 9054 9055 9056 9057 9058 9059 9060 9061 9062 9063 9064 9065

The hinge region

The hinge part right after the last LRR and the part just before TM1 share a good amount of conservation throughout the entire GpHR family. Since a few very conserved and well-studied residues and motifs can be found here, we have numbered these alignable parts of the hinge region. We have divided it in two parts: a stretch after LRR9 and a stretch before TM1.

The key residue of the first part is labeled H50 and is the well-conserved serine of the SHCC motif. From there we number up- and downstream from H38-H61. The key residue of the second part was labeled H150 and chosen to be the aspartate of the well-conserved F/YDY motif. From there we number up- and downstream from H143-H175.

Hinge part 1
Residue F L H L T R A D L S Y P S H C C A F K N Q K K I	Number H38 H39 H40 H41 H42 H43 H44 H45 H46 H47 H48 H49 H50 H51 H52 H53 H54 H55 H56 H57 H58 H59 H60 H61

Hinge part 2
Residue Q A F D S H Y D Y T I C G D S E D M V C T P K S D E F N P C E D I	Number H143 H144 H145 H146 H147 H148 H149 H150 H151 H152 H153 H154 H155 H156 H157 H158 H159 H160 H161 H162 H163 H164 H165 H166 H167 H168 H169 H170 H171 H172 H173 H174 H175