8KF5
The cryo-EM structure of type1 amyloid beta 42 fibril in AD3.
Functional Information from PROSITE/UniProt
| site_id | PS00280 |
| Number of Residues | 19 |
| Details | BPTI_KUNITZ_1 Pancreatic trypsin inhibitor (Kunitz) family signature. FfyGGCggnrnnFdteeyC |
| Chain | Residue | Details |
| D | PHE-352-CYS-334 |
| site_id | PS00319 |
| Number of Residues | 8 |
| Details | APP_CUBD Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. GVEFVCCP |
| Chain | Residue | Details |
| D | GLY-490-PRO-483 |
| site_id | PS00320 |
| Number of Residues | 8 |
| Details | APP_INTRA Amyloid precursor protein (APP) intracellular domain signature. GYENPTYK |
| Chain | Residue | Details |
| D | GLY85-LYS92 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4098 |
| Details | TOPO_DOM: Extracellular => ECO:0000305 |
| Chain | Residue | Details |
| D | LEU-653-ALA30 | |
| C | LEU-653-ALA30 | |
| E | LEU-653-ALA30 | |
| A | LEU-653-ALA30 | |
| F | LEU-653-ALA30 | |
| B | LEU-653-ALA30 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 120 |
| Details | TRANSMEM: Helical => ECO:0000305|PubMed:22584060, ECO:0000305|PubMed:22654059, ECO:0000305|PubMed:30630874 |
| Chain | Residue | Details |
| D | ILE31-MET51 | |
| C | ILE31-MET51 | |
| E | ILE31-MET51 | |
| A | ILE31-MET51 | |
| F | ILE31-MET51 | |
| B | ILE31-MET51 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 282 |
| Details | TOPO_DOM: Cytoplasmic => ECO:0000305 |
| Chain | Residue | Details |
| D | LEU52-ASN99 | |
| C | LEU52-ASN99 | |
| E | LEU52-ASN99 | |
| A | LEU52-ASN99 | |
| F | LEU52-ASN99 | |
| B | LEU52-ASN99 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:8158260 |
| Chain | Residue | Details |
| D | ASN-575 | |
| C | ASN-575 | |
| E | ASN-575 | |
| A | ASN-575 | |
| F | ASN-575 | |
| B | ASN-575 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01217, ECO:0000269|PubMed:17239395, ECO:0000269|PubMed:25122912, ECO:0007744|PDB:2FK1 |
| Chain | Residue | Details |
| D | HIS-524 | |
| F | HIS-520 | |
| B | HIS-524 | |
| B | HIS-520 | |
| D | HIS-520 | |
| C | HIS-524 | |
| C | HIS-520 | |
| E | HIS-524 | |
| E | HIS-520 | |
| A | HIS-524 | |
| A | HIS-520 | |
| F | HIS-524 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01217, ECO:0000269|PubMed:17239395, ECO:0007744|PDB:2FK1 |
| Chain | Residue | Details |
| D | TYR-503 | |
| C | TYR-503 | |
| E | TYR-503 | |
| A | TYR-503 | |
| F | TYR-503 | |
| B | TYR-503 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 18 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:8344894 |
| Chain | Residue | Details |
| D | GLU-488 | |
| A | GLU-488 | |
| A | CYS-485 | |
| A | CYS-484 | |
| F | GLU-488 | |
| F | CYS-485 | |
| F | CYS-484 | |
| B | GLU-488 | |
| B | CYS-485 | |
| B | CYS-484 | |
| D | CYS-485 | |
| D | CYS-484 | |
| C | GLU-488 | |
| C | CYS-485 | |
| C | CYS-484 | |
| E | GLU-488 | |
| E | CYS-485 | |
| E | CYS-484 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11274207, ECO:0000269|PubMed:26898943 |
| Chain | Residue | Details |
| D | HIS6 | |
| F | HIS14 | |
| B | HIS6 | |
| B | HIS14 | |
| D | HIS14 | |
| C | HIS6 | |
| C | HIS14 | |
| E | HIS6 | |
| E | HIS14 | |
| A | HIS6 | |
| A | HIS14 | |
| F | HIS6 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10413512, ECO:0000305|PubMed:11274207 |
| Chain | Residue | Details |
| D | TYR10 | |
| C | TYR10 | |
| E | TYR10 | |
| A | TYR10 | |
| F | TYR10 | |
| B | TYR10 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10413512, ECO:0000269|PubMed:11274207, ECO:0000269|PubMed:26898943 |
| Chain | Residue | Details |
| D | HIS13 | |
| C | HIS13 | |
| E | HIS13 | |
| A | HIS13 | |
| F | HIS13 | |
| B | HIS13 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 6 |
| Details | SITE: Required for Cu(2+) reduction => ECO:0000255|PROSITE-ProRule:PRU01217 |
| Chain | Residue | Details |
| D | MET-501 | |
| C | MET-501 | |
| E | MET-501 | |
| A | MET-501 | |
| F | MET-501 | |
| B | MET-501 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 12 |
| Details | SITE: Cleavage; by caspases => ECO:0000269|PubMed:10319819 |
| Chain | Residue | Details |
| D | ASP-474 | |
| F | ASP-452 | |
| B | ASP-474 | |
| B | ASP-452 | |
| D | ASP-452 | |
| C | ASP-474 | |
| C | ASP-452 | |
| E | ASP-474 | |
| E | ASP-452 | |
| A | ASP-474 | |
| A | ASP-452 | |
| F | ASP-474 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 6 |
| Details | SITE: Reactive bond |
| Chain | Residue | Details |
| D | ARG-370 | |
| C | ARG-370 | |
| E | ARG-370 | |
| A | ARG-370 | |
| F | ARG-370 | |
| B | ARG-370 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by beta-secretase => ECO:0000305|PubMed:11851430 |
| Chain | Residue | Details |
| D | MET0 | |
| C | MET0 | |
| E | MET0 | |
| A | MET0 | |
| F | MET0 | |
| B | MET0 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by caspase-6; when associated with variant 670-N-L-671 |
| Chain | Residue | Details |
| D | ASP1 | |
| C | ASP1 | |
| E | ASP1 | |
| A | ASP1 | |
| F | ASP1 | |
| B | ASP1 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by ACE => ECO:0000269|PubMed:11604391, ECO:0000269|PubMed:16154999 |
| Chain | Residue | Details |
| D | ASP7 | |
| C | ASP7 | |
| E | ASP7 | |
| A | ASP7 | |
| F | ASP7 | |
| B | ASP7 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by alpha-secretase => ECO:0000305|PubMed:11851430 |
| Chain | Residue | Details |
| D | LYS16 | |
| C | LYS16 | |
| E | LYS16 | |
| A | LYS16 | |
| F | LYS16 | |
| B | LYS16 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by theta-secretase => ECO:0000269|PubMed:16816112 |
| Chain | Residue | Details |
| D | PHE19 | |
| C | PHE19 | |
| E | PHE19 | |
| A | PHE19 | |
| F | PHE19 | |
| B | PHE19 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 6 |
| Details | SITE: Implicated in free radical propagation => ECO:0000250 |
| Chain | Residue | Details |
| D | GLY33 | |
| C | GLY33 | |
| E | GLY33 | |
| A | GLY33 | |
| F | GLY33 | |
| B | GLY33 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 6 |
| Details | SITE: Susceptible to oxidation => ECO:0000269|PubMed:10535332 |
| Chain | Residue | Details |
| D | MET35 | |
| C | MET35 | |
| E | MET35 | |
| A | MET35 | |
| F | MET35 | |
| B | MET35 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by gamma-secretase; site 1 => ECO:0000305|PubMed:11851430 |
| Chain | Residue | Details |
| D | VAL40 | |
| C | VAL40 | |
| E | VAL40 | |
| A | VAL40 | |
| F | VAL40 | |
| B | VAL40 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by gamma-secretase; site 2 => ECO:0000305|PubMed:11851430 |
| Chain | Residue | Details |
| D | ALA42 | |
| C | ALA42 | |
| E | ALA42 | |
| A | ALA42 | |
| F | ALA42 | |
| B | ALA42 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by gamma-secretase; site 3 => ECO:0000269|PubMed:11851430, ECO:0000305|PubMed:30630874 |
| Chain | Residue | Details |
| D | LEU49 | |
| C | LEU49 | |
| E | LEU49 | |
| A | LEU49 | |
| F | LEU49 | |
| B | LEU49 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 6 |
| Details | SITE: Cleavage; by caspase-6, caspase-8 or caspase-9 => ECO:0000269|PubMed:10319819 |
| Chain | Residue | Details |
| D | ASP68 | |
| C | ASP68 | |
| E | ASP68 | |
| A | ASP68 | |
| F | ASP68 | |
| B | ASP68 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine; by CK2 => ECO:0000269|PubMed:8999878 |
| Chain | Residue | Details |
| D | SER-473 | |
| C | SER-473 | |
| E | SER-473 | |
| A | SER-473 | |
| F | SER-473 | |
| B | SER-473 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine; by CK1 => ECO:0000269|PubMed:8999878 |
| Chain | Residue | Details |
| D | SER-465 | |
| C | SER-465 | |
| E | SER-465 | |
| A | SER-465 | |
| F | SER-465 | |
| B | SER-465 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 18 |
| Details | MOD_RES: Sulfotyrosine => ECO:0000255 |
| Chain | Residue | Details |
| D | TYR-454 | |
| A | TYR-454 | |
| A | TYR-409 | |
| A | TYR-335 | |
| F | TYR-454 | |
| F | TYR-409 | |
| F | TYR-335 | |
| B | TYR-454 | |
| B | TYR-409 | |
| B | TYR-335 | |
| D | TYR-409 | |
| D | TYR-335 | |
| C | TYR-454 | |
| C | TYR-409 | |
| C | TYR-335 | |
| E | TYR-454 | |
| E | TYR-409 | |
| E | TYR-335 |
| site_id | SWS_FT_FI28 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine; by FAM20C => ECO:0000269|PubMed:26091039 |
| Chain | Residue | Details |
| D | SER-230 | |
| C | SER-230 | |
| E | SER-230 | |
| A | SER-230 | |
| F | SER-230 | |
| B | SER-230 |
| site_id | SWS_FT_FI29 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26091039 |
| Chain | Residue | Details |
| D | TYR-174 | |
| C | TYR-174 | |
| E | TYR-174 | |
| A | TYR-174 | |
| F | TYR-174 | |
| B | TYR-174 |
| site_id | SWS_FT_FI30 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P08592 |
| Chain | Residue | Details |
| D | THR58 | |
| C | THR58 | |
| E | THR58 | |
| A | THR58 | |
| F | THR58 | |
| B | THR58 |
| site_id | SWS_FT_FI31 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine; by APP-kinase I => ECO:0000250|UniProtKB:P08592 |
| Chain | Residue | Details |
| D | SER59 | |
| C | SER59 | |
| E | SER59 | |
| A | SER59 | |
| F | SER59 | |
| B | SER59 |
| site_id | SWS_FT_FI32 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphothreonine; by CDK5 and MAPK10 => ECO:0000269|PubMed:28720718, ECO:0000269|PubMed:8131745, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| D | THR72 | |
| C | THR72 | |
| E | THR72 | |
| A | THR72 | |
| F | THR72 | |
| B | THR72 |
| site_id | SWS_FT_FI33 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:11877420 |
| Chain | Residue | Details |
| D | TYR86 | |
| C | TYR86 | |
| E | TYR86 | |
| A | TYR86 | |
| F | TYR86 | |
| B | TYR86 |
| site_id | SWS_FT_FI34 |
| Number of Residues | 6 |
| Details | CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:16335952 |
| Chain | Residue | Details |
| D | ASN-129 | |
| C | ASN-129 | |
| E | ASN-129 | |
| A | ASN-129 | |
| F | ASN-129 | |
| B | ASN-129 |
| site_id | SWS_FT_FI35 |
| Number of Residues | 6 |
| Details | CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000305 |
| Chain | Residue | Details |
| D | ASN-100 | |
| C | ASN-100 | |
| E | ASN-100 | |
| A | ASN-100 | |
| F | ASN-100 | |
| B | ASN-100 |
| site_id | SWS_FT_FI36 |
| Number of Residues | 18 |
| Details | CARBOHYD: O-linked (GalNAc...) threonine; partial => ECO:0000269|PubMed:21712440, ECO:0000269|PubMed:22576872 |
| Chain | Residue | Details |
| D | THR-38 | |
| A | THR-38 | |
| A | THR-20 | |
| A | THR-19 | |
| F | THR-38 | |
| F | THR-20 | |
| F | THR-19 | |
| B | THR-38 | |
| B | THR-20 | |
| B | THR-19 | |
| D | THR-20 | |
| D | THR-19 | |
| C | THR-38 | |
| C | THR-20 | |
| C | THR-19 | |
| E | THR-38 | |
| E | THR-20 | |
| E | THR-19 |
| site_id | SWS_FT_FI37 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (Xyl...) (chondroitin sulfate) serine; in L-APP isoforms => ECO:0000269|PubMed:21712440 |
| Chain | Residue | Details |
| D | SER-15 | |
| C | SER-15 | |
| E | SER-15 | |
| A | SER-15 | |
| F | SER-15 | |
| B | SER-15 |
| site_id | SWS_FT_FI38 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (HexNAc...) threonine; partial => ECO:0000269|PubMed:22576872 |
| Chain | Residue | Details |
| D | THR-12 | |
| C | THR-12 | |
| E | THR-12 | |
| A | THR-12 | |
| F | THR-12 | |
| B | THR-12 |
| site_id | SWS_FT_FI39 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (GalNAc...) threonine; partial => ECO:0000269|PubMed:22576872, ECO:0000305|PubMed:21712440 |
| Chain | Residue | Details |
| D | THR-8 | |
| C | THR-8 | |
| E | THR-8 | |
| A | THR-8 | |
| F | THR-8 | |
| B | THR-8 |
| site_id | SWS_FT_FI40 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (GalNAc...) serine; partial => ECO:0000269|PubMed:22576872, ECO:0000305|PubMed:21712440 |
| Chain | Residue | Details |
| D | SER-4 | |
| C | SER-4 | |
| E | SER-4 | |
| A | SER-4 | |
| F | SER-4 | |
| B | SER-4 |
| site_id | SWS_FT_FI41 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (HexNAc...) tyrosine; partial => ECO:0000269|PubMed:22576872 |
| Chain | Residue | Details |
| D | TYR10 | |
| C | TYR10 | |
| E | TYR10 | |
| A | TYR10 | |
| F | TYR10 | |
| B | TYR10 |
| site_id | SWS_FT_FI42 |
| Number of Residues | 12 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P08592 |
| Chain | Residue | Details |
| D | LYS92 | |
| B | LYS92 | |
| C | LYS92 | |
| E | LYS92 | |
| A | LYS92 | |
| F | LYS92 |
