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(-) Description

Title :  CRYSTAL STRUCTURE OF ADAPTOR PROTEIN COMPLEX 4 (AP-4) MU4 SUBUNIT C-TERMINAL DOMAIN D190A MUTANT, IN COMPLEX WITH A SORTING PEPTIDE FROM THE AMYLOID PRECURSOR PROTEIN (APP)
 
Authors :  B. H. Ross, Y. Lin, E. A. Corales, P. V. Burgos, G. A. Mardones
Date :  23 Aug 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin-Like Beta-Sandwich, Adaptor Protein Complex, Golgi Apparatus, Sorting Signal Recognition, Alzheimer'S Disease, Amyloid Precursor Protein, Protein Transport-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. H. Ross, Y. Lin, E. A. Corales, P. V. Burgos, G. A. Mardones
Structural And Functional Characterization Of Cargo-Binding Sites On The Mu 4-Subunit Of Adaptor Protein Complex 4.
Plos One V. 9 88147 2014
PubMed-ID: 24498434  |  Reference-DOI: 10.1371/JOURNAL.PONE.0088147

(-) Compounds

Molecule 1 - AP-4 COMPLEX SUBUNIT MU-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINUS, RESIDUES 160-453
    Gene: AP4M1, MUARP2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AP-4 ADAPTER COMPLEX MU SUBUNIT, ADAPTER-RELATED PROTEIN COMPLEX 4 MU-1 SUBUNIT, MU SUBUNIT OF AP-4, MU-ADAPTIN-RELATED PROTEIN 2, MU-ARP2, MU4-ADAPTIN, MU4
 
Molecule 2 - AMYLOID BETA A4 PROTEIN
    Chains: B
    Engineered: YES
    Fragment: C-TERMINUS, RESIDUES 761-767
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synonym: ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II, N- APP, SOLUBLE APP-ALPHA, S-APP-ALPHA, SOLUBLE APP-BETA, S-APP-BETA, C99, BETA-AMYLOID PROTEIN 42, BETA-APP42, BETA-AMYLOID PROTEIN 40, BETA-APP40, C83, P3(42), P3(40), C80, GAMMA-SECRETASE C-TERMINAL FRAGMENT 59, AMYLOID INTRACELLULAR DOMAIN 59, AICD-59, AID(59), GAMMA-CTF(59), GAMMA-SECRETASE C-TERMINAL FRAGMENT 57, AMYLOID INTRACELLULAR DOMAIN 57, AICD-57, AID(57), GAMMA-CTF(57), GAMMA- SECRETASE C-TERMINAL FRAGMENT 50, AMYLOID INTRACELLULAR DOMAIN 50, AICD-50, AID(50), GAMMA-CTF(50), C31
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4MDR)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:254 , PHE A:255 , HIS A:256 , SER A:257 , LEU A:261 , GLU A:265 , THR A:280 , ARG A:283 , ARG A:297 , PHE A:299 , HOH B:701 , HOH B:702 , HOH B:703 , HOH B:704BINDING SITE FOR CHAIN B OF AMYLOID BETA A4 PROTEIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MDR)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:306 -Gly A:307
2Leu A:400 -Gly A:401
3Gly A:403 -Pro A:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MDR)

(-) 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:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee....ee............ee.eeeee......hhhhhheeee....eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeee.....eeeee..eeeeee..ee...eeeeeeeee.......eeeeeeee........eeeeee..eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdr A 185 NEVFLAVVERLSVLIASNGSLLKVDVQGEIRLKSFLPSGSEMRIGLTEEFSVGKSELRGYGPGIRVDEVSFHSSVNLDEFESHRILRLQPPQGELTVMRYQLSDDLPSPLPFRLFPSVQWDRGSGRLQVYLKLRCDLLSKSQALNVRLHLPLPRGVVSLSQELSSPEQKAELAEGALRWDLPRVQGGSQLSGLFQMDVPLGLGPASLSFELPRHTCSGLQVRFLRLAPHKWVRHLSHSDAYVIRI 453
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       400       410       420      |438       448     
                                                                                                                                                                                                                                383|                        427|                 
                                                                                                                                                                                                                                 400                         436                 


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..eee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4mdr B 686 TYKFFEQ 692
   Legend:   → Mismatch (orange background)
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  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 4MDR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (121, 128)

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  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:306 - Gly A:307   [ RasMol ]  
    Gly A:403 - Pro A:404   [ RasMol ]  
    Leu A:400 - Gly A:401   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        A4_HUMAN | P05067: 1aap 1amb 1amc 1aml 1ba4 1ba6 1bjb 1bjc 1brc 1ca0 1hz3 1iyt 1mwp 1owt 1qcm 1qwp 1qxc 1qyt 1taw 1tkn 1uo7 1uo8 1uoa 1uoi 1x11 1z0q 1ze7 1ze9 1zjd 2beg 2bom 2bp4 2fjz 2fk1 2fk2 2fk3 2fkl 2fma 2g47 2ipu 2lfm 2llm 2lmn 2lmo 2lmp 2lmq 2lnq 2loh 2lp1 2lz3 2lz4 2m4j 2m9r 2m9s 2mgt 2mj1 2mpz 2mvx 2mxu 2nao 2otk 2r0w 2wk3 2y29 2y2a 2y3j 2y3k 2y3l 3ayu 3bae 3bkj 3dxc 3dxd 3dxe 3gci 3ifl 3ifn 3ifo 3ifp 3jq5 3jql 3jti 3ktm 3l33 3l81 3moq 3mxc 3mxy 3nyj 3nyl 3ovj 3ow9 3sv1 3u0t 3umh 3umi 3umk 4hix 4jfn 4m1c 4mvi 4mvk 4mvl 4nge 4ojf 4onf 4ong 4pqd 4pwq 4xxd 5aef 5am8 5amb 5buo 5c67 5csz 5how 5hox 5hoy 5kk3 5kna 5myo
        AP4M1_HUMAN | O00189: 3l81

(-) Related Entries Specified in the PDB File

3l81 WILD-TYPE PROTEIN COMPLEXED WITH THE SAME PEPTIDE