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(-) Description

Title :  CRYSTAL STRUCTURE OF APP E2 DOMAIN IN COMPLEX WITH DR6 CRD DOMAIN
 
Authors :  K. Xu, D. Nikolov
Date :  08 Mar 15  (Deposition) - 15 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alzheimer, Neuron Pruning, Amyloid Precursor Protein, Apoptosis-Cell Adhesion Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Xu, O. Olsen, D. Tzvetkova-Robev, M. Tessier-Lavigne, D. B. Nikolo
The Crystal Structure Of Dr6 In Complex With The Amyloid Precursor Protein Provides Insight Into Death Receptor Activation.
Genes Dev. V. 29 785 2015
PubMed-ID: 25838500  |  Reference-DOI: 10.1101/GAD.257675.114

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 21
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 42-220
    Gene: TNFRSF21, DR6
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CYSTEINE RICH DOMAIN OF MOUSE DR6 PROTEIN
    Synonym: DEATH RECEPTOR 6
 
Molecule 2 - AMYLOID BETA A4 PROTEIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 370-592
    Gene: APP
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ABPP,APP,ALZHEIMER DISEASE AMYLOID A4 PROTEIN HOMOLOG, AMYLOIDOGENIC GLYCOPROTEIN,AG

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:150 , PRO A:151 , TRP A:154 , SER A:177 , VAL A:179 , HOH A:441binding site for residue MG A 302
2AC2SOFTWAREASN A:82 , MET A:83binding site for Mono-Saccharide NAG A 301 bound to ASN A 82
3AC3SOFTWAREASN B:467 , SER B:471binding site for Mono-Saccharide NAG B 601 bound to ASN B 467

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:67 -A:80
2A:70 -A:88
3A:91 -A:106
4A:109 -A:123
5A:113 -A:131
6A:133 -A:144
7A:150 -A:168
8A:171 -A:186
9A:192 -A:211

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:115 -Pro A:116
2Val B:408 -Pro B:409

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YN0)

(-) Exons   (0, 0)

(no "Exon" information available for 4YN0)

(-) 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:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee......eeeee.....eeeee........eeee....ee..........ee.........eeee........eee....eeee..eeee.......eeeee........eeee....ee..........ee...hhhhh.eeee........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yn0 A  49 SLPGTYRHVDRTTGQVLTCDKCPAGTYVSEHCTNMSLRVCSSCPAGTFTRHENGIERCHDCSQPCPWPMIERLPCAALTDRECICPPGMYQSNGTCAPHTVCPVGWGVRKKGTENEDVRCKQCARGTFSDVPSSVMKCKAHTDCLGQNLEVVKPGTKETDNVCGMRLF 216
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        


Chain B from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yn0 B 306 TPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPHHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMIS 507
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505
   Legend:   → Mismatch (orange background)
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  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 4YN0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YN0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YN0)

(-) Gene Ontology  (128, 134)

Asymmetric/Biological Unit(hide GO term definitions)

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  4yn0
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 Related Entries

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

UniProtKB/Swiss-Prot
        A4_MOUSE | P12023: 2roz 2ysz 2yt0 2yt1 5myk

(-) Related Entries Specified in the PDB File

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