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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT RABBIT PRP 121-230 (S174N)
 
Authors :  B. Sweeting, A. Chakrabartty, E. F. Pai
Date :  18 Oct 12  (Deposition) - 15 May 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Prp, Prion, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Sweeting, E. Brown, M. Q. Khan, A. Chakrabartty, E. F. Pai
N-Terminal Helix-Cap In Alpha-Helix 2 Modulates Beta-State Misfolding In Rabbit And Hamster Prion Proteins.
Plos One V. 8 63047 2013
PubMed-ID: 23675452  |  Reference-DOI: 10.1371/JOURNAL.PONE.0063047

(-) Compounds

Molecule 1 - MAJOR PRION PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (AI)
    Expression System Taxid: 562
    Expression System Vector Type: PET28A
    Fragment: UNP RESIDUES 119-229
    Gene: PRNP, PRP
    Mutation: YES
    Organism Common: EUROPEAN RABBIT,JAPANESE WHITE RABBIT,DOMESTIC RABBIT,RABBITS
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: PRP, PRP27-30, PRP33-35C

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:136 , ARG A:148BINDING SITE FOR RESIDUE CL A 301
2AC2SOFTWAREGLY A:142 , ASP A:144 , GLU A:152 , HOH A:401 , HOH A:419 , HOH B:435BINDING SITE FOR RESIDUE NA A 302
3AC3SOFTWARETYR A:145 , ARG A:151 , HOH A:405 , HOH A:406 , TYR B:226 , ALA B:230 , HOH B:413BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREARG B:136 , ARG B:148BINDING SITE FOR RESIDUE CL B 301
5AC5SOFTWAREGLY B:142 , ASP B:144 , GLU B:152 , HOH B:408 , HOH B:453 , HOH B:461BINDING SITE FOR RESIDUE NA B 302
6AC6SOFTWAREARG B:228 , HOH B:406 , HOH B:416 , HOH B:423 , HOH B:436 , HOH B:450BINDING SITE FOR RESIDUE NA B 303
7AC7SOFTWAREARG A:164 , HIS A:177 , 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 304
8AC8SOFTWARELEU B:138 , ILE B:139 , ASP B:147 , TYR B:150 , ARG B:151BINDING SITE FOR RESIDUE GOL B 305

(-) 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 A:126 -Gly A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HMM)

(-) 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
                                                                                                                                 
               SCOP domains d4hmma_ A: automated matches                                                                      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
                 4hmm A 126 GGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQQES 222
                                   135       145       155       165       175       185       195       205       215       


Chain B from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains d4hmmb_ B: automated matches                                                                              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
                 4hmm B 126 GGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTVTTTTKGENFTETDIKIMERVVEQMCITQYQQESQAAYQRAA 230
                                   135       145       155       165       175       185       195       205       215       225
   Legend:   → Mismatch (orange background)
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  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 4HMM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRIO_RABIT | Q95211: 2fj3 2joh 2jom 4hls 4hmr

(-) Related Entries Specified in the PDB File

3o79 WILD-TYPE RABBIT PRP
4hls MUTANT RABBIT PRP (S170N)
4hmr