Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  ATOMIC-RESOLUTION STRUCTURE OF A TRIPLET 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 :  12.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J,K,L  (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
    ChainsA, B, C, D, E, F, G, H, I, J, K, L
    EngineeredYES
    FragmentRESIDUES 125-135
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPREALBUMIN, TBPA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (114x)ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2M5M)

(-) Sites  (0, 0)

(no "Site" information available for 2M5M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M5M)

(-) PROSITE Motifs  (1, 12)

Asymmetric Unit (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSTHYRETIN_2PS00769 Transthyretin signature 2.TTHY_RAT125-137
 
 
 
 
 
 
 
 
 
 
 
  12A:1-11
B:1-11
C:1-11
D:1-11
E:1-11
F:1-11
G:1-11
H:1-11
I:1-11
J:1-11
K:1-11
L:1-11
Biological Unit 1 (1, 1368)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSTHYRETIN_2PS00769 Transthyretin signature 2.TTHY_RAT125-137
 
 
 
 
 
 
 
 
 
 
 
  1368A:1-11
B:1-11
C:1-11
D:1-11
E:1-11
F:1-11
G:1-11
H:1-11
I:1-11
J:1-11
K:1-11
L:1-11

(-) Exons   (1, 12)

Asymmetric Unit (1, 12)
 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_RAT113-1473512A:1-11
B:1-11
C:1-11
D:1-11
E:1-11
F:1-11
G:1-11
H:1-11
I:1-11
J:1-11
K:1-11
L:1-11
11
11
11
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
                 2m5m 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
                 2m5m 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
                 2m5m 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
                 2m5m 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
                 2m5m 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
                 2m5m 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
                 2m5m 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
                 2m5m H   1 YTIAALLSPYS  11
                                    10 

Chain I 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
                 2m5m I   1 YTIAALLSPYS  11
                                    10 

Chain J 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
                 2m5m J   1 YTIAALLSPYS  11
                                    10 

Chain K 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
                 2m5m K   1 YTIAALLSPYS  11
                                    10 

Chain L 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
                 2m5m L   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 2M5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M5M)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2m5m)
 
  Sites
(no "Sites" information available for 2m5m)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2m5m)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2m5m
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TTHY_RAT | P02767
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TTHY_RAT | P02767
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TTHY_RAT | P027671gke 1ie4 1kgi 1kgj 1rvs 2m5k 3zpk

(-) Related Entries Specified in the PDB File

2m5k 2m5n 3zpk