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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE RABBIT PRP 126-230
 
Authors :  B. Sweeting, A. Chakrabartty, E. F. Pai
Date :  30 Jul 10  (Deposition) - 24 Nov 10  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Prp, Prion, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Q. Khan, B. Sweeting, V. K. Mulligan, P. E. Arslan, N. R. Cashman, E. F. Pai, A. Chakrabartty
Prion Disease Susceptibility Is Affected By Beta-Structure Folding Propensity And Local Side-Chain Interactions In Prp
Proc. Natl. Acad. Sci. Usa V. 107 19808 2010
PubMed-ID: 21041683  |  Reference-DOI: 10.1073/PNAS.1005267107

(-) Compounds

Molecule 1 - RABBIT PRP
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(AI)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 127-231
    Gene: PRNP
    Organism Common: EUROPEAN RABBIT,JAPANESE WHITE RABBIT,DOMESTIC RABBIT,RABBITS
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:55 , ARG A:156 , ASN A:197 , ASP A:202BINDING SITE FOR RESIDUE NA A 2
2AC2SOFTWAREHOH A:11 , HOH A:36 , HOH A:90 , GLY A:142 , ASP A:144 , GLU A:152BINDING SITE FOR RESIDUE NA A 3
3AC3SOFTWAREARG A:136 , ARG A:148BINDING SITE FOR RESIDUE CL A 1
4AC4SOFTWAREHOH B:44 , HOH B:94 , GLY B:142 , ASP B:144 , GLU B:152 , HOH B:275BINDING SITE FOR RESIDUE NA B 1
5AC5SOFTWAREHOH A:79 , HOH A:91 , HOH B:19 , HOH B:31 , HOH B:96 , ARG B:228BINDING SITE FOR RESIDUE NA B 4
6AC6SOFTWAREARG B:136 , ARG B:148BINDING SITE FOR RESIDUE CL B 2
7AC7SOFTWAREARG A:164 , ASP A:178 , ASN A:181 , TYR B:128 , ARG B:164 , HIS B:177 , ASP B:178 , ASN B:181BINDING SITE FOR RESIDUE GOL B 231
8AC8SOFTWARELEU B:138 , ILE B:139 , HIS B:140 , ASP B:147 , TYR B:150 , ARG B:151BINDING SITE FOR RESIDUE GOL B 232
9AC9SOFTWAREHOH A:17 , TYR A:145 , HOH B:12 , TYR B:226 , ALA B:230BINDING SITE FOR RESIDUE GOL B 233

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:179 -A:214
2B:179 -B:214

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:126 -Gly B:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O79)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O79)

(-) Exons   (0, 0)

(no "Exon" information available for 3O79)

(-) 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:97
 aligned with Q9TSF8_RABIT | Q9TSF8 from UniProtKB/TrEMBL  Length:254

    Alignment length:97
                                   136       146       156       166       176       186       196       206       216       
         Q9TSF8_RABIT   127 GGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQQES 223
               SCOP domains d3o79a_ A: Prion protein domain                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee............hhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3o79 A 126 GGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQQES 222
                                   135       145       155       165       175       185       195       205       215       


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with Q9TSF8_RABIT | Q9TSF8 from UniProtKB/TrEMBL  Length:254

    Alignment length:105
                                   136       146       156       166       176       186       196       206       216       226     
         Q9TSF8_RABIT   127 GGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQQESQAAYQRAA 231
               SCOP domains d3o79b_ B: Prion protein domain                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee............hhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3o79 B 126 GGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQQESQAAYQRAA 230
                                   135       145       155       165       175       185       195       205       215       225
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O79)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O79)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9TSF8_RABIT | Q9TSF8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3o79
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