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(-) Description

Title :  CRYO-EM STRUCTURE OF THE HUMAN GAMMA-SECRETASE COMPLEX AT 3.4 ANGSTROM RESOLUTION.
 
Authors :  X. Bai, C. Yan, G. Yang, P. Lu, D. Ma, L. Sun, R. Zhou, S. H. W. Scheres, Y. Sh
Date :  24 Jun 15  (Deposition) - 05 Aug 15  (Release) - 28 Dec 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Cryo-Em, Human Gamma-Secretase, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Bai, C. Yan, G. Yang, P. Lu, D. Ma, L. Sun, R. Zhou, S. H. W. Scheres, Y. Shi
An Atomic Structure Of Human Gamma-Secretase
Nature V. 525 212 2015
PubMed-ID: 26280335  |  Reference-DOI: 10.1038/NATURE14892

(-) Compounds

Molecule 1 - NICASTRIN
    Cell Line: HEK 293F
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Expression System Vector: PMLINK
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PRESENILIN-1
    Cell Line: HEK 293F
    Chains: B
    EC Number: 3.4.23.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Expression System Vector: PMLINK
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PS-1, PROTEIN S182, PRESENILIN
 
Molecule 3 - GAMMA-SECRETASE SUBUNIT APH-1A
    Cell Line: HEK 293F
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Expression System Vector: PMLINK
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APH-1A, APH-1ALPHA, PRESENILIN-STABILIZATION FACTOR, APH-1
 
Molecule 4 - GAMMA-SECRETASE SUBUNIT PEN-2
    Cell Line: HEK 293F
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Expression System Vector: PMLINK
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PRESENILIN ENHANCER PROTEIN 2, PEN-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PC12Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL B:94 , ALA B:98 , LYS B:101 , TRP B:404 , PHE B:411 , PHE C:6 , ILE C:135 , ALA C:139 , LEU C:142BINDING SITE FOR RESIDUE PC1 B 1468
02AC2SOFTWAREILE A:690 , PHE A:698 , THR C:24 , ARG C:31 , ARG C:115 , GLN C:116 , TYR C:119 , LEU C:169 , PHE C:173BINDING SITE FOR RESIDUE PC1 C 1245
03AC3SOFTWAREPRO A:43 , ASN A:45 , GLU A:188Binding site for Poly-Saccharide residues NAG A1699 through NAG A1700 bound to ASN A 45
04AC4SOFTWAREASN A:55 , ALA A:56 , HIS A:58 , PHE A:145 , TYR A:173 , GLU A:174Binding site for Poly-Saccharide residues NAG A1701 through BMA A1718 bound to ASN A 55
05AC5SOFTWAREASP A:185 , ASN A:187Binding site for Mono-Saccharide NAG A1715 bound to ASN A 187
06AC6SOFTWAREASN A:264 , THR A:266 , GLY A:267 , ASN A:596 , ASP A:598Binding site for Mono-Saccharide NAG A1714 bound to ASN A 264
07AC7SOFTWAREASN A:387 , VAL A:390Binding site for Mono-Saccharide NAG A1705 bound to ASN A 387
08AC8SOFTWARETYR A:152 , VAL A:383 , LYS A:386 , ASN A:387 , ARG A:432 , ASN A:435Binding site for Poly-Saccharide residues NAG A1703 through NAG A1704 bound to ASN A 435
09AC9SOFTWAREASN A:464Binding site for Mono-Saccharide NAG A1712 bound to ASN A 464
10BC1SOFTWAREASN A:506Binding site for Mono-Saccharide NAG A1713 bound to ASN A 506
11BC2SOFTWAREASN A:530Binding site for Poly-Saccharide residues NAG A1708 through NAG A1709 bound to ASN A 530
12BC3SOFTWAREGLN A:552 , ASN A:562Binding site for Poly-Saccharide residues NAG A1710 through NAG A1711 bound to ASN A 562
13BC4SOFTWAREARG A:520 , TRP A:533 , ASN A:573 , GLY A:576 , VAL A:578 , ARG A:619 , VAL A:621Binding site for Poly-Saccharide residues NAG A1706 through NAG A1707 bound to ASN A 573

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:50 -A:62
2A:140 -A:159
3A:195 -A:213
4A:230 -A:248

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A63)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A63)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A63)

(-) Exons   (0, 0)

(no "Exon" information available for 5A63)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhheeee..eee...ee....eeee.......eeeeeee.hhhhhhhhhh......eeeee.....hhhhhhhhhhh......eeee............................hhhhh.................ee...eeee.hhhhhhhhhhhhhhhh..........eeeeeeee.......hhhhhhhhhhhhhhh.......eee..eeeeeee...............eeeeeee................hhhhhhhhhhhhhhhhhh........eeeeeee........hhhhhhhhhhhh........eeeeeeee........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhh...eeeee................hhhhhh.........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh......hhhhh..hhhhhh..............hhhhhhhhhhhhhhhheee..hhhhhhh............eeeee.............eeeee...eeee.hhhhhh...........eee.....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a63 A  34 NSVERKIYIPLNKTAPCVRLLNATHQIGCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAGLAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPIFLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTFSINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVASFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVDSFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQPLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFVTDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQDLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLYEYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARIFLIASKELELITLTVGFGILIFSLIVTYCINAKADVLF 698
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693     


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a63 B  78 GAKHVIMLFVPVTLCMVVVVATIKSVSFYTRIISSLLLLFFFSFIYLGEVFKTYNVAVDYITVALLIWNFGVVGMISIHWKGPLRLQQAYLIMISALMALVFIKYLPEWTAWLILAVISVYDLVAVVKLGLGDFIFYSVLVGKASATASGDWNTTIACFVAILIGLCLTLLLLAIFKKALPALPISITFGLVFYFATDYLVQPFMDQLAFHQFYI 467
                                    87        97       107||     175       185       195       205       215       225       235       245       255     ||382       392       402       412       422       432       442       452       462     
                                                        108|                                                                                           261|                                                                                        
                                                         167                                                                                            379                                                                                        


Chain C from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a63 C   2 GAAVFFGCTFVAFGPAFALFLITVAGDPLRVIILVAGAFFWLVSLLLASVVWFILVHVTDRSDARLQYGLLIFGAAVSVLLQEVFRFAYYKLLKKADEGLASLSEDGRSPISIRQMAYVSGLSFGIISGVFSVINILADALGPGVVGIHGDSPYYFLTSAFLTAAIILLHTFWGVVFFDACERRRYWALGLVVGSHLLTSGLTFLNPWYEASLLPIYAVTVSMGLWAFITAGGSLRSIQRSLL 244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   


Chain D from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5a63 D   2 NLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLVPAYTEQSQIKGYVWRSAVGFLFWVIVLTSWITIFQIYRPRWGALGDYLSFTIPLGTP 101
                                    11        21        31        41        51        61        71        81        91       101
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5A63)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A63)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A63)

(-) Gene Ontology  (141, 198)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a63
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  APH1A_HUMAN | Q96BI3
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  NICA_HUMAN | Q92542
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  PEN2_HUMAN | Q9NZ42
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  PSN1_HUMAN | P49768
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  3.4.23.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        APH1A_HUMAN | Q96BI3: 5fn2 5fn3 5fn4 5fn5
        NICA_HUMAN | Q92542: 2n7q 2n7r 4uis 5fn2 5fn3 5fn4 5fn5
        PEN2_HUMAN | Q9NZ42: 5fn2 5fn3 5fn4 5fn5
        PSN1_HUMAN | P49768: 2kr6 4uis 5fn2 5fn3 5fn4 5fn5

(-) Related Entries Specified in the PDB File

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