8OQY: Nicastrin

Structure of apo form of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc. Determined by electron microscopy at 3.3 Å resolution. Released 24 Apr 2024.

Method
Electron microscopy
Resolution
3.3 Å
Organism
Homo sapiens
Chains
4
Atoms
9,809
Mol. weight
178.59 kDa
Ligands
PC1, NAG
Released
24 Apr 2024

Explore 8OQY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OQY contains 57 α-helices and 33 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.

Chain A: 31 helices, 30 β-strands

ElementResiduesLengthSheet
α-helix35-395
β-strand42-4321
β-strand47-4931
α-helix50-512
β-strand53-5422
β-strand59-6022
β-strand61-6223
β-strand69-7351
α-helix79-868
β-strand94-9961
α-helix105-1139
β-strand120-12451
α-helix125-1262
β-strand13514
α-helix154-1563
β-strand16814
α-helix171-1733
β-strand175-17623
β-strand180-18341
α-helix186-19914
α-helix207-2093
β-strand212-21761
α-helix227-23913
β-strand248-25032
β-strand253-25975
β-strand275-28175
α-helix295-2995
α-helix300-31314
α-helix318-3203
β-strand324-33075
α-helix338-34811
α-helix356-3583
β-strand359-36575
β-strand375-37955
α-helix384-3863
α-helix388-40619
β-strand412-41435
α-helix421-4233
α-helix427-4315
β-strand438-44255
α-helix460-4634
α-helix473-4775
α-helix482-50120
α-helix515-52612
α-helix532-5354
β-strand53916
α-helix540-5456
α-helix562-57514
β-strand577-57936
α-helix583-5875
α-helix589-5913
β-strand601-60556
β-strand60917
β-strand61617
β-strand619-62356
β-strand626-63055
α-helix633-6364
β-strand649-65132
β-strand658-66361
α-helix666-69227
α-helix694-6974
Chain B: 11 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix74-10330
α-helix162-18928
β-strand193-19428
α-helix195-21319
α-helix219-24022
α-helix243-2453
α-helix246-25510
α-helix384-39714
α-helix405-42723
α-helix437-44812
α-helix449-4535
α-helix454-4629
Chain C: 9 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix3-2422
α-helix25-273
α-helix29-6032
α-helix65-9935
α-helix113-13725
α-helix138-1403
β-strand14511
α-helix155-18228
α-helix186-20520
α-helix209-23022
Chain D: 6 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix8-2114
α-helix27-4115
α-helix50-8132
α-helix83-853
α-helix87-926
β-strand93-9428
α-helix96-972

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
NicastrinAprotein717Homo sapiensQ92542 (AlphaFold model)
Presenilin-1 CTF12Bprotein467Homo sapiensP49768 (AlphaFold model)
Gamma-secretase subunit APH-1BCprotein257Homo sapiensQ8WW43 (AlphaFold model)
Gamma-secretase subunit PEN-2Dprotein101Homo sapiensQ9NZ42 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8OQY_1 Nicastrin (chains A)
MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQI
GCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAG
LAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPI
FLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTF
SINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVA
SFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVD
SFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQ
PLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFV
TDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQ
DLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLY
EYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARI
FLIASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSYGTLEVLFQ
Sequence of entity 2 (B), FASTA
>8OQY_2 Presenilin-1 CTF12 (chains B)
MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSR
QVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTE
DTETVGQRALHSILNAAIMISVIVVMTILLVVLYKYRCYKVIHAWLIISSLLLLFFFSFI
YLGEVFKTYNVAVDYITVALLIWNFGVVGMISIHWKGPLRLQQAYLIMISALMALVFIKY
LPEWTAWLILAVISVYDLVAVLCPKGPLRMLVETAQERNETLFPALIYSSTMVWLVNMAE
GDPEAQRRVSKNSKYNAESTERESQDTVAENDDGGFSEEWEAQRDSHLGPHRSTPESRAA
VQELSSSILAGEDPEERGVKLGLGDFIFYSVLVGKASATASGDWNTTIACFVAILIGLCL
TLLLLAIFKKALPALPISITFGLVFYFATDYLVQPFMDQLAFHQFYI
Sequence of entity 3 (C), FASTA
>8OQY_3 Gamma-secretase subunit APH-1B (chains C)
MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVII
DNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVS
GLGFGIMSGVFSFVNTLSDSLGPGTVGIHGDSPQFFLYSAFMTLVIILLHVFWGIVFFDG
CEKKKWGILLIVLLTHLLVSAQTFISSYYGINLASAFIILVLMGTWAFLAAGGSCRSLKL
CLLCQDKNFLLYNQRSR
Sequence of entity 4 (D), FASTA
>8OQY_4 Gamma-secretase subunit PEN-2 (chains D)
MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRS
AVGFLFWVIVLTSWITIFQIYRPRWGALGDYLSFTIPLGTP

Ligands and cofactors

IDNameFormulaCopies
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P3
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O67

Primary citation

Apo and A beta 46-bound gamma-secretase structures provide insights into amyloid-beta processing by the APH-1B isoform. Odorcic, I., Hamed, M.B., Lismont, S. et al. Nat Commun (2024) 15:4479-4479. DOI 10.1038/s41467-024-48776-2 · PubMed

Other PDB entries of the same protein (UniProt Q92542 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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