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(-) Description

Title :  STRUCTURE OF POM1 FAB FRAGMENT COMPLEXED WITH MOUSE PRPC FRAGMENT 120-230
 
Authors :  P. K. Baral, B. Wieland, M. Swayampakula, M. N. James
Date :  21 Sep 12  (Deposition) - 31 Jul 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  C-Term Mouse Prion Protein, Pom1 Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sonati, R. R. Reimann, J. Falsig, P. K. Baral, T. O'Connor, S. Hornemann, S. Yaganoglu, B. Li, U. S. Herrmann, B. Wieland, M. Swayampakula, M. H. Rahman, D. Das, N. Kav, R. Riek, P. P. Liberski, M. N. James, A. Aguzzi
The Toxicity Of Antiprion Antibodies Is Mediated By The Flexible Tail Of The Prion Protein.
Nature V. 501 102 2013
PubMed-ID: 23903654  |  Reference-DOI: 10.1038/NATURE12402

(-) Compounds

Molecule 1 - MAJOR PRION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERM FRAGMENT
    Gene: PRNP, PRN-P, PRP
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PRP, PRP27-30, PRP33-35C
 
Molecule 2 - POM1 FAB CHAIN H
    Cell: HYBRIDOMA
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - POM1 FAB CHAIN L
    Cell: HYBRIDOMA
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER H:191 , SER H:195 , GLU H:196 , GLU L:79 , GLU L:81BINDING SITE FOR RESIDUE NA L 301

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:178 -A:213
2H:22 -H:96
3H:145 -H:200
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe H:151 -Pro H:152
2Glu H:153 -Pro H:154
3Trp H:193 -Pro H:194
4Ser L:7 -Pro L:8
5Trp L:94 -Pro L:95
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H88)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H88)

(-) Exons   (0, 0)

(no "Exon" information available for 4H88)

(-) 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:102
                                                                                                                                      
               SCOP domains d4h88a_ A: automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee............hhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4h88 A 124 LGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVVTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY 225
                                   133       143       153       163       173       183       193       203       213       223  


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee.........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h88 H   1 QVQLQQSGTELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGSIDPSDSYTSHNEKFKGKATLTVDESSSTAYMQLSSLTSEDSAVYFCSRSGYGYYAMEYWGQGTSVTVSSAKTTPPSVYPLAPGGGATNSMVTLGCLVKGYFPEPVTVTWNSGSLSGGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4h88l1 L:1-107 automated matches                                                                          d4h88l2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h88 L   1 DIVLTQSPAILSVSPGERVSFSCRASQNIGTSIHWYQQRTNESPRLIIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQSNTWPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTLTKDEYERHNTYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H88)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H88)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:153 - Pro H:154   [ RasMol ]  
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    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:193 - Pro H:194   [ RasMol ]  
    Trp L:94 - Pro L:95   [ RasMol ]  
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  4h88
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  PRIO_MOUSE | P04925
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRIO_MOUSE | P04925: 1ag2 1xyx 1y15 1y16 2k5o 2kfm 2kfo 2ku5 2ku6 2l1d 2l1e 2l1h 2l1k 2l39 2l40 3nvg 3nvh 4j8r 4ma7 4ma8

(-) Related Entries Specified in the PDB File

4dgi STRUCTURE OF POM1 FAB FRAGMENT COMPLEXED WITH MOUSE PRPC FRAGMENT 120-230