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(-) Description

Title :  CRYSTAL STRUCTURE OF DEER PRION PROTEIN COMPLEXED WITH POM1 FAB
 
Authors :  P. K. Baral, M. Swayampakula, M. N. G. James
Date :  23 Mar 15  (Deposition) - 23 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  H,L  (1x)
Keywords :  Prion, Antibody, Immune System Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Baral, M. Swayampakula, A. Aguzzi, M. N. James
X-Ray Structural And Molecular Dynamical Studies Of The Globular Domains Of Cow, Deer, Elk And Syrian Hamster Prion Proteins.
J. Struct. Biol. V. 192 37 2015
PubMed-ID: 26320075  |  Reference-DOI: 10.1016/J.JSB.2015.08.014

(-) Compounds

Molecule 1 - MAJOR PRION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRNP, PRP
    Organism Common: MULE DEER
    Organism Scientific: ODOCOILEUS HEMIONUS
    Organism Taxid: 9872
    Synonym: PRP
 
Molecule 2 - POM1 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - POM1 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AHL
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/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  (4, 4)

Asymmetric Unit
No.Residues
1A:171 -A:206
2H:22 -H:96
3H:145 -H:200
4L:23 -L:88

(-) Cis Peptide Bonds  (6, 6)

Asymmetric 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 4YXH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YXH)

(-) 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:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee............hhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4yxh A 117 LGGYMLGSAMNRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYNNQNTFVHDCVNITVKQHTVTTTTKGENFTETDIKMMERVVEQMCITQYQRESQAY 217
                                   126       136       146       156       166       176       186       196       206       216 


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee.........eeeeeeeeeee.....eeee.......eeee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yxh 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee...................eeeee.........eeeeeeeeeehhhhhh.....ee..........ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yxh 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)
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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 4YXH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  4yxh
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4YXH)

(-) Related Entries Specified in the PDB File

4yx2 4yxk 4yxl