Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution. Determined by electron microscopy at 3.4 Å resolution. Released 5 Aug 2015.
Explore 5A63 in 3D Show helices and sheets RCSB PDB PDBe
5A63 contains 60 α-helices and 35 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 35-40 | 6 | |
| β-strand | 41-44 | 4 | 1 |
| β-strand | 47-49 | 3 | 1 |
| β-strand | 53-54 | 2 | 2 |
| β-strand | 59-60 | 2 | 2 |
| β-strand | 61-62 | 2 | 3 |
| β-strand | 64 | 1 | 4 |
| α-helix | 65 | 1 | |
| β-strand | 70-76 | 7 | 1 |
| α-helix | 79-86 | 8 | |
| β-strand | 94-99 | 6 | 1 |
| α-helix | 105-113 | 9 | |
| β-strand | 121-124 | 4 | 1 |
| α-helix | 154-156 | 3 | |
| β-strand | 175-176 | 2 | 3 |
| β-strand | 180-183 | 4 | 1 |
| α-helix | 186-199 | 14 | |
| β-strand | 203 | 1 | 5 |
| β-strand | 207 | 1 | 5 |
| β-strand | 211-218 | 8 | 1 |
| β-strand | 220 | 1 | 4 |
| β-strand | 221 | 1 | 6 |
| α-helix | 227-239 | 13 | |
| β-strand | 248-250 | 3 | 2 |
| β-strand | 253-259 | 7 | 7 |
| α-helix | 268-270 | 3 | |
| β-strand | 275-281 | 7 | 7 |
| α-helix | 295-300 | 6 | |
| α-helix | 301-314 | 14 | |
| β-strand | 324-330 | 7 | 7 |
| α-helix | 340-349 | 10 | |
| β-strand | 359-366 | 8 | 7 |
| β-strand | 375-379 | 5 | 7 |
| α-helix | 382-386 | 5 | |
| α-helix | 388-406 | 19 | |
| β-strand | 412-414 | 3 | 7 |
| α-helix | 420-423 | 4 | |
| α-helix | 426-433 | 8 | |
| β-strand | 438-442 | 5 | 7 |
| α-helix | 460-463 | 4 | |
| α-helix | 475-478 | 4 | |
| α-helix | 482-502 | 21 | |
| α-helix | 515-526 | 12 | |
| α-helix | 535-537 | 3 | |
| α-helix | 542-545 | 4 | |
| α-helix | 562-575 | 14 | |
| β-strand | 577-579 | 3 | 8 |
| α-helix | 583-587 | 5 | |
| β-strand | 601-605 | 5 | 8 |
| α-helix | 608-609 | 2 | |
| β-strand | 610 | 1 | 9 |
| β-strand | 615 | 1 | 9 |
| β-strand | 619-623 | 5 | 8 |
| β-strand | 627-630 | 4 | 7 |
| α-helix | 633-636 | 4 | |
| β-strand | 649-651 | 3 | 2 |
| α-helix | 652 | 1 | |
| β-strand | 653 | 1 | 6 |
| β-strand | 657-664 | 8 | 1 |
| α-helix | 665 | 1 | |
| α-helix | 666-692 | 27 | |
| α-helix | 694-697 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 79-103 | 25 | |
| α-helix | 105-107 | 3 | |
| α-helix | 168-172 | 5 | |
| α-helix | 173-177 | 5 | |
| α-helix | 178-189 | 12 | |
| β-strand | 193-194 | 2 | 10 |
| α-helix | 195-214 | 20 | |
| α-helix | 219-240 | 22 | |
| α-helix | 243-259 | 17 | |
| α-helix | 380-382 | 3 | |
| α-helix | 383-398 | 16 | |
| α-helix | 405-427 | 23 | |
| α-helix | 436-448 | 13 | |
| α-helix | 449-453 | 5 | |
| α-helix | 454-463 | 10 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 3-20 | 18 | |
| α-helix | 21-25 | 5 | |
| α-helix | 29-60 | 32 | |
| α-helix | 65-101 | 37 | |
| α-helix | 102-106 | 5 | |
| α-helix | 114-141 | 28 | |
| α-helix | 145-146 | 2 | |
| α-helix | 156-184 | 29 | |
| α-helix | 187-205 | 19 | |
| α-helix | 210-231 | 22 | |
| α-helix | 236-242 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 3-5 | 3 | |
| α-helix | 8-21 | 14 | |
| α-helix | 27-35 | 9 | |
| α-helix | 38-43 | 6 | |
| α-helix | 50-84 | 35 | |
| α-helix | 87-92 | 6 | |
| β-strand | 93-95 | 3 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Nicastrin | A | protein | 709 | Homo sapiens | Q92542 (AlphaFold model) |
| Presenilin-1 | B | protein | 467 | Homo sapiens | P49768 (AlphaFold model) |
| Gamma-secretase subunit APH-1A | C | protein | 265 | Homo sapiens | Q96BI3 (AlphaFold model) |
| Gamma-secretase subunit PEN-2 | D | protein | 101 | Homo sapiens | Q9NZ42 (AlphaFold model) |
>5A63_1 Nicastrin (chains A) MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQI GCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAG LAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPI FLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTF SINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVA SFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVD SFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQ PLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFV TDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQ DLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLY EYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARI FLIASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
>5A63_2 Presenilin-1 (chains B) MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSR QVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTE DTETVGQRALHSILNAAIMISVIVVMTILLVVLYKYRCYKVIHAWLIISSLLLLFFFSFI YLGEVFKTYNVAVDYITVALLIWNFGVVGMISIHWKGPLRLQQAYLIMISALMALVFIKY LPEWTAWLILAVISVYDLVAVLCPKGPLRMLVETAQERNETLFPALIYSSTMVWLVNMAE GDPEAQRRVSKNSKYNAESTERESQDTVAENDDGGFSEEWEAQRDSHLGPHRSTPESRAA VQELSSSILAGEDPEERGVKLGLGDFIFYSVLVGKASATASGDWNTTIACFVAILIGLCL TLLLLAIFKKALPALPISITFGLVFYFATDYLVQPFMDQLAFHQFYI
>5A63_3 Gamma-secretase subunit APH-1A (chains C) MGAAVFFGCTFVAFGPAFALFLITVAGDPLRVIILVAGAFFWLVSLLLASVVWFILVHVT DRSDARLQYGLLIFGAAVSVLLQEVFRFAYYKLLKKADEGLASLSEDGRSPISIRQMAYV SGLSFGIISGVFSVINILADALGPGVVGIHGDSPYYFLTSAFLTAAIILLHTFWGVVFFD ACERRRYWALGLVVGSHLLTSGLTFLNPWYEASLLPIYAVTVSMGLWAFITAGGSLRSIQ RSLLCRRQEDSRVMVYSALRIPPED
>5A63_4 Gamma-secretase subunit PEN-2 (chains D) MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRS AVGFLFWVIVLTSWITIFQIYRPRWGALGDYLSFTIPLGTP
| ID | Name | Formula | Copies |
|---|---|---|---|
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 2 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 5 |
An Atomic Structure of Human Gamma-Secretase. Bai, X., Yan, C., Yang, G. et al. Nature (2015) 525:212. DOI 10.1038/NATURE14892 · PubMed
Other PDB entries of the same protein (UniProt Q92542 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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