PDB entry 6idf

View 6idf on RCSB PDB site
Description: cryo-em structure of gamma secretase in complex with a notch fragment
Deposited on 2018-09-09, released 2018-12-26
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-02.
Experiment type: EM
Resolution: 2.7 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: nicastrin
    Species: Homo sapiens [TaxId:9606]
    Gene: NCSTN
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Presenilin-1
    Species: Homo sapiens [TaxId:9606]
    Gene: PS1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P49768 (Start-466)
      • engineered mutation (111)
      • engineered mutation (384)
  • Chain 'C':
    Compound: gamma-secretase subunit aph-1a
    Species: Homo sapiens [TaxId:9606]
    Gene: APH1A
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: gamma-secretase subunit pen-2
    Species: Homo sapiens [TaxId:9606]
    Gene: PEN2
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Notch1
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IDF
  • Heterogens: NAG, PC1, CLR

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6idfA (A:)
matagggsgadpgsrgllrllsfcvllaglcrgnsverkiyiplnktapcvrllnathqi
gcqssisgdtgvihvvekeedlqwvltdgpnppymvlleskhftrdlmeklkgrtsriag
lavsltkpspasgfspsvqcpndgfgvysnsygpefahcreiqwnslgnglayedfsfpi
flledenetkvikqcyqdhnlsqngsaptfplcamqlfshmhavistatcmrrssiqstf
sinpeivcdplsdynvwsmlkpinttgtlkpddrvvvaatrldsrsffwnvapgaesava
sfvtqlaaaealqkapdvttlprnvmfvffqgetfdyigssrmvydmekgkfpvqlenvd
sfvelgqvalrtslelwmhtdpvsqknesvrnqvedllatleksgagvpavilrrpnqsq
plppsslqrflrarnisgvvladhsgafhnkyyqsiydtaeninvsypewlspeedlnfv
tdtakaladvatvlgralyelaggtnfsdtvqadpqtvtrllygflikannswfqsilrq
dlrsylgdgplqhyiavssptnttyvvqyalanltgtvvnltreqcqdpskvpsenkdly
eyswvqgplhsnetdrlprcvrstarlaralspafelsqwssteystwtesrwkdirari
fliaskelelitltvgfgilifslivtycinakadvlfiaprepgavsy

    Sequence, based on observed residues (ATOM records):
    >6idfA (A:)
nsverkiyiplnktapcvrllnathqigcqssisgdtgvihvvekeedlqwvltdgpnpp
ymvlleskhftrdlmeklkgrtsriaglavsltkpspasgfspsvqcpndgfgvysnsyg
pefahcreiqwnslgnglayedfsfpiflledenetkvikqcyqdhnlsqngsaptfplc
amqlfshmhavistatcmrrssiqstfsinpeivcdplsdynvwsmlkpinttgtlkpdd
rvvvaatrldsrsffwnvapgaesavasfvtqlaaaealqkapdvttlprnvmfvffqge
tfdyigssrmvydmekgkfpvqlenvdsfvelgqvalrtslelwmhtdpvsqknesvrnq
vedllatleksgagvpavilrrpnqsqplppsslqrflrarnisgvvladhsgafhnkyy
qsiydtaeninvsypewlspeedlnfvtdtakaladvatvlgralyelaggtnfsdtvqa
dpqtvtrllygflikannswfqsilrqdlrsylgdgplqhyiavssptnttyvvqyalan
ltgtvvnltreqcqdpskvpsenkdlyeyswvqgplhsnetdrlprcvrstarlaralsp
afelsqwssteystwtesrwkdirarifliaskelelitltvgfgilifslivtycinak
advlfia

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6idfB (B:)
mtelpaplsyfqnaqmsednhlsntvrsqndnrerqehndrrslghpeplsngrpqgnsr
qvveqdeeedeeltlkygakhvimlfvpvtlcmvvvvatiksvsfytrkdgcliytpfte
dtetvgqralhsilnaaimisvivvmtillvvlykyrcykvihawliissllllfffsfi
ylgevfktynvavdyitvalliwnfgvvgmisihwkgplrlqqaylimisalmalvfiky
lpewtawlilavisvydlvavlcpkgplrmlvetaqernetlfpaliysstmvwlvnmae
gdpeaqrrvsknskynaesteresqdtvaenddggfseeweaqrdshlgphrstpesraa
vqelsssilagedpeergvklglgafifysvlvgkasatasgdwnttiacfvailiglcl
tllllaifkkalpalpisitfglvfyfatdylvqpfmdqlafhqfyi

    Sequence, based on observed residues (ATOM records):
    >6idfB (B:)
ltlkygakhvimlfvpvtlcmvvvvatiksvsfytrkdgcliytpftedtetvgqralhs
ilnaaimisvivvmtillvvlykyrcykvihawliissllllfffsfiylgevfktynva
vdyitvalliwnfgvvgmisihwkgplrlqqaylimisalmalvfikylpewtawlilav
isvydlvavlcpkgplrmlvetaqernetlfpaliysstmergvklglgafifysvlvgk
asatasgdwnttiacfvailiglcltllllaifkkalpalpisitfglvfyfatdylvqp
fmdqlafhqfyi

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6idfC (C:)
mgaavffgctfvafgpafalflitvagdplrviilvagaffwlvslllasvvwfilvhvt
drsdarlqygllifgaavsvllqevfrfayykllkkadeglaslsedgrspisirqmayv
sglsfgiisgvfsviniladalgpgvvgihgdspyyfltsafltaaiillhtfwgvvffd
acerrrywalglvvgshlltsgltflnpwyeasllpiyavtvsmglwafitaggslrsiq
rsllcrrqedsrvmvysalripped

    Sequence, based on observed residues (ATOM records):
    >6idfC (C:)
gaavffgctfvafgpafalflitvagdplrviilvagaffwlvslllasvvwfilvhvtd
rsdarlqygllifgaavsvllqevfrfayykllkkadeglaslsedgrspisirqmayvs
glsfgiisgvfsviniladalgpgvvgihgdspyyfltsafltaaiillhtfwgvvffda
cerrrywalglvvgshlltsgltflnpwyeasllpiyavtvsmglwafitaggslrsiqr
sll

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6idfD (D:)
mnlervsneeklnlcrkyylggfaflpflwlvnifwffreaflvpayteqsqikgyvwrs
avgflfwvivltswitifqiyrprwgalgdylsftiplgtp

    Sequence, based on observed residues (ATOM records):
    >6idfD (D:)
nlervsneeklnlcrkyylggfaflpflwlvnifwffreaflvpayteqsqikgyvwrsa
vgflfwvivltswitifqiyrprwgalgdylsftiplgtp

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6idfE (E:)
mvqsetvecpppaqlhfmyvaaaafvllffvgcgvllsrkrrrqhgqlwfpegfkvseas
kkkrreplgedsvglkplknasdgalmddnqnewgdedleteqkliseedllesdevdai
ehhhhhhhh

    Sequence, based on observed residues (ATOM records):
    >6idfE (E:)
vqsetvecpppaqlhfmyvaaaafvllffvgcgvllsrkrr