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(-) Description

Title :  STRUCTURE OF AN OCTAPEPTIDE REPEAT OF THE PRION PROTEIN BOUND TO THE POM2 FAB ANTIBODY FRAGMENT
 
Authors :  M. Swayampakula, P. K. Baral, N. N. V. Kav, A. Aguzzi, M. N. G. James
Date :  14 Feb 13  (Deposition) - 22 May 13  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,I,J
Biol. Unit 1:  A,B,I  (1x)
Biol. Unit 2:  C,D,J  (1x)
Keywords :  Immunoglobulin Fold, Fab, Antibody, Octapeptide Repeat, Mouse Prion Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Swayampakula, P. K. Baral, A. Aguzzi, N. N. Kav, M. N. James
The Crystal Structure Of An Octapeptide Repeat Of The Prion Protein In Complex With A Fab Fragment Of The Pom2 Antibody
Protein Sci. V. 22 893 2013
PubMed-ID: 23629842  |  Reference-DOI: 10.1002/PRO.2270

(-) Compounds

Molecule 1 - LIGHT CHAIN OF POM2 FAB
    Chains: A, C
    Fragment: UNP RESIDUES 67-82
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - HEAVY CHAIN OF POM2 FAB
    Chains: B, D
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - MAJOR PRION PROTEIN
    Chains: I, J
    Engineered: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PRP, PRP27-30, PRP33-35C
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDIJ
Biological Unit 1 (1x): AB  I 
Biological Unit 2 (1x):   CD J

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4J8R)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:90 , ASN B:58 , PRO B:100 , THR B:100A , TYR B:100B , TYR B:100C , ALA B:100D , HOH I:101BINDING SITE FOR CHAIN I OF MAJOR PRION PROTEIN
2AC2SOFTWARETYR C:48 , TRP C:49 , TYR C:90 , TYR D:32 , ASN D:58 , GLY D:96 , ALA D:97 , PRO D:100 , THR D:100A , TYR D:100B , TYR D:100C , ALA D:100D , ASP D:101BINDING SITE FOR CHAIN J OF MAJOR PRION PROTEIN

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:87
2A:132 -A:192
3B:22 -B:92
4B:139 -B:194
5C:23 -C:87
6C:132 -C:192
7D:22 -D:92
8D:139 -D:194

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Tyr A:138 -Pro A:139
2Ser B:54 -Gly B:55
3Ala B:127 -Ala B:128
4Ala B:130 -Ala B:131
5Phe B:145 -Pro B:146
6Glu B:147 -Pro B:148
7Trp B:187 -Pro B:188
8Trp I:6 -Gly I:7
9Tyr C:138 -Pro C:139
10Ala D:129 -Ala D:130
11Phe D:145 -Pro D:146
12Glu D:147 -Pro D:148
13Trp D:187 -Pro D:188
14Trp J:6 -Gly J:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J8R)

(-) Exons   (0, 0)

(no "Exon" information available for 4J8R)

(-) 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:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j8r A    1 DIVMTQSHKFMSTSVGDRVSITCKASQVGTALAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLSDYFCQQYSSYPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee.........ee...eeeee........eeeee.........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhhhhh..eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j8r B    2 VKLQESGGEVVRPGTSVKVSCKASGYAFTNYLIEWVKQRPGQGLEWIGVINPGSGDTNYNEKFKGKATLTADKSSSTAYMQLNSLTSDDSAVYFCARSGAAAPTYYAMDYWGQGVSVTVSSAKTTPPSVYPLAPAAAAANSMVTLGCLVKGYFPEPVTVTWNSGSLSGGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  212
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||102       112       122       132       142       152       162       172       182       192       202       212
                                                                             52A                            82A||               100A||||                                                                                                                
                                                                                                             82B|                100B|||                                                                                                                
                                                                                                              82C                 100C||                                                                                                                
                                                                                                                                   100D|                                                                                                                
                                                                                                                                    100E                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4j8r C    1 DIVMTQSHKFMSTSVGDRVSITCKASQVGTALAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLSDYFCQQYSSYPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRA  210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee.........ee...eeeee........eeeee..........eeeeeeeeee.....eeee........eee...eee..eeeeeeeeeehhhhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j8r D    2 VKLQESGGEVVRPGTSVKVSCKASGYAFTNYLIEWVKQRPGQGLEWIGVINPGSGDTNYNEKFKGKATLTADKSSSTAYMQLNSLTSDDSAVYFCARSGAAAPTYYAMDYWGQGVSVTVSSAKTTPPSVYPLAPAAAAANSMVTLGCLVKGYFPEPVTVTWNSGSLSGGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  212
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||102       112       122       132       142       152       162       172       182       192       202       212
                                                                             52A                            82A||               100A||||                                                                                                                
                                                                                                             82B|                100B|||                                                                                                                
                                                                                                              82C                 100C||                                                                                                                
                                                                                                                                   100D|                                                                                                                
                                                                                                                                    100E                                                                                                                


Chain I 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
                4j8r I    1 PHGGSWGQP    9


Chain J from PDB  Type:PROTEIN  Length:8
                                         
               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
                4j8r J    1 PHGGSWGQ    8
   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 4J8R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J8R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J8R)

(-) Gene Ontology  (40, 40)

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  Cis Peptide Bonds
    Ala B:127 - Ala B:128   [ RasMol ]  
    Ala B:130 - Ala B:131   [ RasMol ]  
    Ala D:129 - Ala D:130   [ RasMol ]  
    Glu B:147 - Pro B:148   [ RasMol ]  
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    Phe D:145 - Pro D:146   [ RasMol ]  
    Ser B:54 - Gly B:55   [ RasMol ]  
    Trp B:187 - Pro B:188   [ RasMol ]  
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    Trp I:6 - Gly I:7   [ RasMol ]  
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    Tyr A:138 - Pro A:139   [ RasMol ]  
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UniProtKB/Swiss-Prot
        PRIO_MOUSE | P04925: 1ag2 1xyx 1y15 1y16 2k5o 2kfm 2kfo 2ku5 2ku6 2l1d 2l1e 2l1h 2l1k 2l39 2l40 3nvg 3nvh 4h88 4ma7 4ma8

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