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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED LIPOCALIN (ANTICALIN H1GA) IN COMPLEX WITH THE ALZHEIMER AMYLOID PEPTIDE ABETA1-40
 
Authors :  A. Eichinger, A. Skerra
Date :  24 Sep 13  (Deposition) - 12 Aug 15  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Beta-Barrel, Engineered Lipocalin, Binding Protein, Protein Binding- Protein Fibril Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Rauth, D. Hinz, M. Borger, M. Uhrig, M. Mayhaus, M. Riemenschneider A. Skerra
High-Affinity Anticalins With Aggregation-Blocking Activity Directed Against The Alzheimer Beta-Amyloid Peptide.
Biochem. J. V. 473 1563 2016
PubMed-ID: 27029347  |  Reference-DOI: 10.1042/BCJ20160114

(-) Compounds

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNGAL98-H1GA
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 21-198
    Gene: ENGINEERED VARIANT H1GA, HNL, LCN2, LCN2 (NGAL_HUMAN), NGAL
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NGAL, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED SUBUNIT OF MMP-9, LIPOCALIN-2, ONCOGENE 24P3, SIDEROCALIN LCN2, P25
 
Molecule 2 - BETA-AMYLOID PROTEIN 40
    Chains: E, F, G, H
    Engineered: YES
    Fragment: UNP RESIDUES 672-711
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE ABETA(1-40) PEPTIDE WAS SYNTHESIZED WITHOUT MODIFICATIONS.
    Synonym: BETA-APP40
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4MVL)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:76 -A:175
2B:76 -B:175
3C:76 -C:175
4D:76 -D:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MVL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MVL)

(-) Sequences/Alignments

Asymmetric 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:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeeeeeeee.............eeeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee..........eeeeeeeee....eeeeeeeee......eeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvl A   5 SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGAAGNVLLREDKDPLKMYATIYELKEDKSYNVTSVGFDDKKCLYKIRTFVPGSQPGEFTLGRIKSEPGGTSWLVRVVSTNYNQHAMVFFKEVAQNRETFNITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eee...........eeeeeeeee....eeeeeeeee......eeeeeee.....hhhhhhhhhhhhhh...hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvl B   6 DLIPAPPLSKVPLQQNFQDNQFHGKWYVVGAAGNVLLREDKDPLKMYATIYELKEDKSYNVTSVGFDDKKCLYKIRTFVPGSQPGEFTLGRIKSEPGGTSWLVRVVSTNYNQHAMVFFKEVAQNRETFNITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee............eeeeeee....eeeeeee........eeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mvl C   5 SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGAAGNVLLREDKDPLKMYATIYELKEDKSYNVTSVGFDDKKCLYKIRTFVPGSQPGEFTLGRIKSEPGGTSWLVRVVSTNYNQHAMVFFKEVAQNRETFNITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhheeeeeeeeee.............eeeeeee.....eeeeeeee....eeeeeeeeee.....eeee..........eeeeeeeee....eeeeeeeee......eeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvl D   7 LIPAPPLSKVPLQQNFQDNQFHGKWYVVGAAGNVLLREDKDPLKMYATIYELKEDKSYNVTSVGFDDKKCLYKIRTFVPGSQPGEFTLGRIKSEPGGTSWLVRVVSTNYNQHAMVFFKEVAQNRETFNITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176 


Chain E from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4mvl E  17 LVFFAEDVGSN  27
                                    26 


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4mvl F  17 LVFFAEDVGSN  27
                                    26 


Chain G from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4mvl G  18 VFFAEDVGS  26


Chain H from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4mvl H  18 VFFAEDVGS  26
   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 4MVL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (121, 126)

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  4mvl
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  NGAL_HUMAN | P80188
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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 4mdr 4mvi 4mvk 4nge 4ojf 4onf 4ong 4pqd 4pwq 4xxd 5aef 5am8 5amb 5buo 5c67 5csz 5how 5hox 5hoy 5kk3 5kna 5myo
        NGAL_HUMAN | P80188: 1dfv 1l6m 1ngl 1qqs 1x71 1x89 1x8u 3by0 3cbc 3cmp 3dsz 3dtq 3fw4 3fw5 3hwd 3hwe 3hwf 3hwg 3i0a 3k3l 3pec 3ped 3t1d 3tf6 3tzs 3u03 3u0d 4gh7 4iaw 4iax 4k19 4mvi 4mvk 4qae 4zfx 4zhc 4zhd 4zhf 4zhg 4zhh 5jr8 5khp 5kic 5kid

(-) Related Entries Specified in the PDB File

4mvi CRYSTAL STRUCTURE OF AN ENGINEERED LIPOCALIN (ANTICALIN US7) IN COMPLEX WITH THE ALZHEIMER AMYLOID PEPTIDE ABETA(1- 40
4mvk CRYSTAL STRUCTURE OF AN ENGINEERED LIPOCALIN (ANTICALIN US7) IN COMPLEX WITH THE ALZHEIMER AMYLOID PEPTIDE FRAGMENT VFFAED