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(-) Description

Title :  ATOMIC-RESOLUTION STRUCTURE OF A DOUBLET CROSS-BETA AMYLOID FIBRIL
 
Authors :  A. W. P. Fitzpatrick, G. T. Debelouchina, M. J. Bayro, D. K. Clare, M. A. C V. S. Bajaj, C. P. Jaroniec, L. Wang, V. Ladizhansky, S. Muller, C. E. Ma C. A. Waudby, H. R. Mott, A. De Simone, T. P. J. Knowles, H. R. Saibil, M. Vendruscolo, E. V. Orlova, R. G. Griffin, C. M. Dobson
Date :  27 Feb 13  (Deposition) - 04 Dec 13  (Release) - 04 Dec 13  (Revision)
Method :  SOLID-STATE NMR; ELECTRON MICROSCOPY
Resolution :  12.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (114x)
Keywords :  Amyloid Fibril, Cross-Beta Structure, Protein Fibril (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. W. Fitzpatrick, G. T. Debelouchina, M. J. Bayro, D. K. Clare, M. A. Caporini, V. S. Bajaj, C. P. Jaroniec, L. Wang, V. Ladizhansky, S. A. Muller, C. E. Macphee, C. A. Waudby, H. R. Mott, A. De Simone, T. P. Knowles, H. R. Saibil, M. Vendruscolo, E. V. Orlova, R. G. Griffin C. M. Dobson
Atomic Structure And Hierarchical Assembly Of A Cross-Beta Amyloid Fibril.
Proc. Natl. Acad. Sci. Usa V. 110 5468 2013
PubMed-ID: 23513222  |  Reference-DOI: 10.1073/PNAS.1219476110

(-) Compounds

Molecule 1 - TRANSTHYRETIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Fragment: UNP RESIDUES 125-135
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PREALBUMIN, TBPA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (114x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2M5K)

(-) Sites  (0, 0)

(no "Site" information available for 2M5K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M5K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M5K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M5K)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSTHYRETIN_2PS00769 Transthyretin signature 2.TTHY_RAT125-137
 
 
 
 
 
 
 		  8A:1-11
B:1-11
C:1-11
D:1-11
E:1-11
F:1-11
G:1-11
H:1-11
Biological Unit 1 (1, 912)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSTHYRETIN_2PS00769 Transthyretin signature 2.TTHY_RAT125-137
 
 
 
 
 
 
 		  912A:1-11
B:1-11
C:1-11
D:1-11
E:1-11
F:1-11
G:1-11
H:1-11

(-) Exons   (1, 8)

Asymmetric Unit (1, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000221131ENSRNOE00000155027chr18:12406551-1240664898TTHY_RAT1-23230--
1.2ENSRNOT000000221132ENSRNOE00000155619chr18:12407695-12407825131TTHY_RAT24-67440--
1.3ENSRNOT000000221133ENSRNOE00000156091chr18:12410367-12410502136TTHY_RAT67-112460--
1.4ENSRNOT000000221134ENSRNOE00000156567chr18:12413430-12413680251TTHY_RAT113-147358A:1-11
B:1-11
C:1-11
D:1-11
E:1-11
F:1-11
G:1-11
H:1-11		11
11
11
11
11
11
11
11

(-) 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:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k A   1 YTIAALLSPYS  11
                                    10 


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k B   1 YTIAALLSPYS  11
                                    10 


Chain C from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k C   1 YTIAALLSPYS  11
                                    10 


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k D   1 YTIAALLSPYS  11
                                    10 


Chain E from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k E   1 YTIAALLSPYS  11
                                    10 


Chain F from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k F   1 YTIAALLSPYS  11
                                    10 


Chain G from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k G   1 YTIAALLSPYS  11
                                    10 


Chain H from PDB  Type:PROTEIN  Length:11
 aligned with TTHY_RAT | P02767 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:11
                                   134 
             TTHY_RAT   125 YTIAALLSPYS 135
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE TRANSTHYRET PROSITE
               Transcript 1 Exon 1.4    Transcript 1
                 2m5k H   1 YTIAALLSPYS  11
                                    10
   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 2M5K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M5K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M5K)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (TTHY_RAT | P02767)
molecular function
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    GO:0042562    hormone binding    Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0070324    thyroid hormone binding    Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland.
biological process
    GO:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0042403    thyroid hormone metabolic process    The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine.
    GO:0070327    thyroid hormone transport    The directed movement of thyroid hormone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TTHY_RAT | P02767: 1gke 1ie4 1kgi 1kgj 1rvs 2m5m 3zpk

(-) Related Entries Specified in the PDB File

2m5m 2m5n 3zpk