7Y5T: PS1-containing gamma-secretase

CryoEM structure of PS1-containing gamma-secretase in complex with MRK-560. Determined by electron microscopy at 2.9 Å resolution. Released 2 Nov 2022.

Method
Electron microscopy
Resolution
2.9 Å
Organism
Homo sapiens
Chains
4
Atoms
10,844
Mol. weight
179.87 kDa
Ligands
NAG, PC1, IGD, CLR
Released
2 Nov 2022

Explore 7Y5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y5T contains 61 α-helices and 34 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: 30 helices, 29 β-strands

ElementResiduesLengthSheet
α-helix37-393
β-strand42-4321
β-strand47-4931
β-strand53-5422
β-strand59-6022
β-strand6113
β-strand69-7681
α-helix81-833
α-helix84-885
β-strand94-9961
α-helix100-1023
α-helix105-1139
β-strand118-12471
α-helix125-1262
β-strand13514
β-strand16814
α-helix171-1733
β-strand17513
β-strand181-18331
α-helix186-19914
α-helix207-2093
β-strand212-21871
α-helix227-24014
β-strand248-25032
β-strand253-25975
β-strand275-28175
α-helix295-2995
α-helix300-31314
β-strand324-33075
α-helix338-34710
β-strand359-36575
β-strand375-37955
α-helix384-3863
α-helix388-40619
β-strand412-41435
α-helix422-4232
α-helix427-4304
β-strand437-44265
α-helix473-4775
α-helix479-4813
α-helix482-50221
α-helix515-52612
α-helix540-5456
α-helix550-5523
α-helix562-57514
β-strand57716
α-helix583-5875
α-helix589-5913
β-strand601-60556
β-strand60917
α-helix6101
β-strand61617
β-strand619-62356
β-strand626-63055
α-helix633-6364
β-strand649-65132
β-strand657-66371
α-helix666-69227
α-helix694-6974
Chain B: 14 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix83-10220
α-helix125-15531
α-helix159-17113
α-helix172-1765
α-helix177-18812
β-strand193-19428
α-helix195-21420
α-helix219-23921
α-helix243-26220
α-helix269-2779
β-strand287-28829
β-strand381-38229
α-helix383-39816
α-helix405-42824
α-helix435-44814
α-helix449-4535
α-helix454-4629
Chain C: 11 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix3-1311
α-helix15-206
α-helix21-255
α-helix29-5931
α-helix66-10136
α-helix114-13825
β-strand14611
α-helix156-18328
α-helix187-20216
α-helix203-2053
α-helix211-23222
α-helix236-2405
Chain D: 6 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix8-2013
α-helix21-233
α-helix27-359
α-helix39-424
α-helix50-8031
α-helix88-914
β-strand93-9538

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
NicastrinAprotein709Homo sapiensQ92542 (AlphaFold model)
Presenilin-1Bprotein467Homo sapiensP49768 (AlphaFold model)
Gamma-secretase subunit APH-1ACprotein265Homo sapiensQ96BI3 (AlphaFold model)
Gamma-secretase subunit PEN-2Dprotein101Homo sapiensQ9NZ42 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7Y5T_1 Nicastrin (chains A)
MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQI
GCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAG
LAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPI
FLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTF
SINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVA
SFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVD
SFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQ
PLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFV
TDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQ
DLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLY
EYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARI
FLIASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
Sequence of entity 2 (B), FASTA
>7Y5T_2 Presenilin-1 (chains B)
MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSR
QVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTE
DTETVGQRALHSILNAAIMISVIVVMTILLVVLYKYRCYKVIHAWLIISSLLLLFFFSFI
YLGEVFKTYNVAVDYITVALLIWNFGVVGMISIHWKGPLRLQQAYLIMISALMALVFIKY
LPEWTAWLILAVISVYDLVAVLCPKGPLRMLVETAQERNETLFPALIYSSTMVWLVNMAE
GDPEAQRRVSKNSKYNAESTERESQDTVAENDDGGFSEEWEAQRDSHLGPHRSTPESRAA
VQELSSSILAGEDPEERGVKLGLGDFIFYSVLVGKASATASGDWNTTIACFVAILIGLCL
TLLLLAIFKKALPALPISITFGLVFYFATDYLVQPFMDQLAFHQFYI
Sequence of entity 3 (C), FASTA
>7Y5T_3 Gamma-secretase subunit APH-1A (chains C)
MGAAVFFGCTFVAFGPAFALFLITVAGDPLRVIILVAGAFFWLVSLLLASVVWFILVHVT
DRSDARLQYGLLIFGAAVSVLLQEVFRFAYYKLLKKADEGLASLSEDGRSPISIRQMAYV
SGLSFGIISGVFSVINILADALGPGVVGIHGDSPYYFLTSAFLTAAIILLHTFWGVVFFD
ACERRRYWALGLVVGSHLLTSGLTFLNPWYEASLLPIYAVTVSMGLWAFITAGGSLRSIQ
RSLLCRRQEDSRVMVYSALRIPPED
Sequence of entity 4 (D), FASTA
>7Y5T_4 Gamma-secretase subunit PEN-2 (chains D)
MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRS
AVGFLFWVIVLTSWITIFQIYRPRWGALGDYLSFTIPLGTP

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O66
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P2
IGD~{N}-[4-[2,5-bis(fluoranyl)phenyl]-4-(4-chlorophenyl)sulfonyl-cyclohexyl]-1,1,1…C19 H17 Cl F5 N O4 S21
CLRCholesterolC27 H46 O3

Primary citation

Molecular basis for isoform-selective inhibition of presenilin-1 by MRK-560. Guo, X., Wang, Y., Zhou, J. et al. Nat Commun (2022) 13:6299-6299. DOI 10.1038/s41467-022-33817-5 · PubMed

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

Browse structure collections

About this viewer

MolViewer shows 7Y5T directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.