------------------------------------------------------------------------------ SWISS-PROT Protein Sequence Data Bank. Release 36.0, July 1998 ------------------------------------------------------------------------------ Nomenclature of extracellular domains ------------------------------------------------------------------------------ Amos Bairoch Email: bairoch@medecine.unige.ch Swiss Institute of Bioinformatics and University of Geneva Switzerland ------------------------------------------------------------------------------ Document name: EXTRADOM.TXT ------------------------------------------------------------------------------ Nomenclature proposal for domains (or modules) found mainly in extracellular proteins of higher eukaryotes. The content of this document has been approved by the participants of the International Workshop on Sequence, Structure, Function and Evolution of Extracellular protein Modules (Sep. 24-28 1994, Margretetrop, Sweden) and has been published as a special poster in TIBS: Bork P., Bairoch A. Extracellular protein modules: a proposed nomenclature. Trends Biochem. Sci. 20:Special poster supplement TIBSC02(1995). All inquiries about extracellular protein modules should be sent by email to: bork@embl-heidelberg.de Graphical reprentations of the modular structure of extracellular proteins is available from the following WWW page: http://www.bork.embl-heidelberg.de/Modules A graphical reprentation of the document you are currently reading is available as: http://www.bork.embl-heidelberg.de/Modules/01-nomenclature.gif Some useful references: [ 1] Baron M., Norman D.G., Campbell I.D. Trends Biochem. Sci. 16:13-17(1991). [ 2] Bork P. FEBS Lett. 286:47-54(1991). [ 3] Bork P. Curr. Opin. Struct. Biol. 2:413-421(1992). [ 4] Doolittle R.F., Bork P. Sci. Am. 269(4):50-56(1993). [ 5] Patthy L. Curr. Opin. Struct. Biol. 1:351-361(1991). Abbreviat. Full name 3D Size Nb SWISS-PROT domain name PROSITE 5C 2C (aa) Cys entry ----------- --------------------------------- -- ---- ----- ----------------------- --------- ANATO AT Anaphylatoxin + 70 6 ANAPHYLATOXIN-LIKE PDOC00906 APPLE AP Apple - 90 4 APPLE PDOC00376 C1Q CQ Complement C1q C-terminal - 140 0-3 C1Q PDOC00857 C345C C3 Complement C3/4/5 C-terminal - 180 4-8 C345C CADHE CA Cadherin + 110 0 CADHERIN PDOC00205 CCP CP CCP (Sushi) (SCR) + 70 4 CCP CLECT CL C-type lectin (CTL) + 130 4/6 C-TYPE LECTIN PDOC00537 COL4C C4 Collagen IV C-terminal - 110 6 COL4C COLFI CF Fibrillar collagens C-terminal - 240 8 FIBRILLAR COLLAGENS CTCK CK C-terminal cystine knot + 90 6/11 CTCK PDOC00912 CUB CU CUB - 110 2/4 CUB PDOC00908 CYSTA CY Cystatin-like + 100 0-4 CYSTATIN-LIKE CYTR CR Cytokine receptor N-terminal + 90 4/6 CYTOKINE RECEPTORS N-T PDOC00214 EGF EG EGF-like + 40 6 EGF-LIKE PDOC00021 FA58A FA Coagulation factors 5/8 type A + 330 2-4 F5/8 TYPE A FA58C FC Coagulation factors 5/8 type C - 150 0-2 F5/8 TYPE C PDOC00988 FBG FG Fibrinogen beta/gamma C-terminal + 250 4 FIBRINOGEN BETA/GAMMA PDOC00445 FIMAC FM Factor I/MAC proteins C6/7 - 70 8/12 FIMAC FN1 F1 Fibronectin type-I + 40 4 FIBRONECTIN TYPE-I PDOC00965 FN2 F2 Fibronectin type-II + 60 4 FIBRONECTIN TYPE-II PDOC00022 FN3 F3 Fibronectin type-III + 90 0 FIBRONECTIN TYPE-III FOLLI FS Follistatin-like + 50 10 FOLLISTATIN-LIKE FURIN FU Furin-like Cys-rich - 170 26 FURIN-LIKE GLA GA Gamma-carboxy-glutamate domain + 60 2 GLA PDOC00011 HEMOP HX Hemopexin-like + 60 0-2 HEMOPEXIN-LIKE PDOC00023 IBPNT IB IGFBP/CTGF N-terminal - 70 12 IGFB/CTGF PDOC00194 IGSF IG Immunoglobulin "superfamily" + 100 0-6 IG-LIKE PDOC00262 IGC1 I1 Immunoglobulin C1 + 100 0-6 IG-LIKE C-TYPE IGC2 I2 Immunoglobulin C2 + 100 0-6 IG-LIKE C2-TYPE IGV IV Immunoglobulin V + 100 0-6 IG-LIKE V-TYPE KRING KR Kringle + 80 6 KRINGLE PDOC00020 KUNIT KU Kunitz/BPTI inhibitor + 60 4/6 KUNITZ/BPTI INHIBITOR PDOC00252 LAMD4 L4 Laminin domain IV (B-type) - 190 0 LAMININ DOMAIN IV LAMEG LE Laminin EGF-like + 50 8 LAMININ EGF-LIKE PDOC00961 LAMG LG Laminin G-like (A-type module) - 190 0-4 LAMININ G-LIKE LAMNT LN Laminin N-terminal (domain VI) - 250 4/6 LAMININ N-TERMINAL LDLRA LA LDL-receptor class A + 40 6 LDL-RECEPTOR CLASS A PDOC00929 LDLRY LY LDL-receptor YWTD motif - 50 0 LDL-RECEPTOR YWTD MOTIF LINK LK Link (Hyaluronan-binding) + 100 4 LINK PDOC00955 LRR LR Leucine-rich repeat + 25 0 LRR LRRC LC LRR C-flank - 60 4 LRR C-FLANK LRRN LP LRR preceeding domain (N-flank) - 40 2/4 LRR N-FLANK LY6UP LU Ly6 antigen/uPA receptor + 70 8/10 LY6/UPAR PDOC00756 MACPF MA MAC proteins/perforin - 250 8 MAC/PERFORIN MAM MM MAM - 170 4 MAM PDOC00604 NOTLI NL Notch/Lin-12 - 30 6 NOTCH/LIN-12 PDOM PD P-type (Trefoil) (TFF) + 50 6 P-TYPE PDOC00024 PKD PK PKD1-like - 80 0 PKD SAPOA SA Saposins-like type A - 30 4 SAPOSINS-LIKE TYPE A SAPOB SB Saposins-like type B - 80 6 SAPOSINS-LIKE TYPE B SEA SE SEA - 80 0 SEA SOMAB SO Somatomedin B - 40 8 SOMATOMEDIN-B LIKE PDOC00453 SRCR SR Scavenger receptor Cys-rich - 110 6 SRCR TGFBP TB TGF-beta binding protein - 70 8 TGFBP THYG1 TY Thyroglobulin type-I - 50 6/8 THYROGLOBULIN TYPE-I PDOC00377 TNFRC TR TNF family receptors Cys-rich + 40 6/8 TNFR-CYS PDOC00561 TSPN TN Thrombospondin (TSP) N-terminal - 210 2/4 TSP N-TERMINAL TSP1 T1 Thrombospondin (TSP) type-I - 60 4/6 TSP TYPE-1 VWFA VA von Willebrand factor type A - 200 0-2 VWFA VWFB VB von Willebrand factor type B - 30 8 VWFB VWFC VC von Willebrand factor type C - 110 10 VWFC PDOC00928 VWFD VD von Willebrand factor type D - 350 28-32 VWFD WAP WA WAP (4-disulfide core) + 50 8 WAP PDOC00026 ZONAP ZP Zona pellucida domain - 310 8/10 ZP PDOC00577 Notes: - The two character abbreviations should only be used for "cartoon" representation of the domain structure of extracellular proteins - The five character abbreviations are intended for use in the text, abstract and non-cartoon figures of articles. Additional 2 letter abbreviations which can be used in cartoon representations of proteins: AN Ankyrin domain C2 C2 domain CC Coiled-coil region CO Collagen-type region DG Diacylglycerol/phorbol ester binding domain EF EF-hand calcium binding loop KH KH domain PH PH domain S2 SH2 domain S3 SH3 domain SI Signal sequence TM Transmembrane region Codes for frequently occuring enzyme modules: [2.7.1.-] Serine/threonine protein kinase [2.7.1.112] Tyrosine protein kinase [3.4.21.-] Trypsin-type serine protease [3.4.24.-] Zinc metallopeptidase [3.1.3.48] Tyrosine protein phosphatase ------------------------------------------------------------------------------