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(-) Description

Title :  ALTERED DIMER INTERFACE DECREASES STABILITY IN AN AMYLOIDOGENIC KAPPA1 BENCE JONES PROTEIN.
 
Authors :  J. R. Thompson, M. Ramirez-Alvarado, E. M. Baden
Date :  24 May 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Al, Light Chain Amyloidosis, Amyloid, Immunoglobulin, Light Chain, Light Chain Variable Domain, Protein Fibril (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Baden, B. A. Owen, F. C. Peterson, B. F. Volkman, M. Ramirez-Alvarado, J. R. Thompson
Altered Dimer Interface Decreases Stability In An Amyloidogenic Protein.
J. Biol. Chem. V. 283 15853 2008
PubMed-ID: 18400753  |  Reference-DOI: 10.1074/JBC.M705347200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMYLOIDOGENIC IMMUNOGLOBULIN LIGHT CHAIN PROTEIN AL-09
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET12A
    Expression System Strain: BL21 GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MUTANT OF VK1 O18/O8 GERMLINE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR D:56 , HOH D:128 , HOH D:157BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:88
2B:23 -B:88
3C:23 -C:88
4D:23 -D:88

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Leu A:94 -Pro A:95
3Ser B:7 -Pro B:8
4Leu B:94 -Pro B:95
5Ser C:7 -Pro C:8
6Leu C:94 -Pro C:95
7Ser D:7 -Pro D:8
8Leu D:94 -Pro D:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q1E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q1E)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q1E)

(-) 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:109
 aligned with A2NI60_HUMAN | A2NI60 from UniProtKB/TrEMBL  Length:108

    Alignment length:109
                              1                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98         
         A2NI60_HUMAN     - --DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
               SCOP domains d2q1ea_ A: automated matches                                                                                  SCOP domains
               CATH domains 2q1eA00 A:-1-107 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2q1e A  -1 ATDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYHCQQYDNLPYTFGQGTKLEIK 107
                                     8        18        28        38        48        58        68        78        88        98         


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with A2NI60_HUMAN | A2NI60 from UniProtKB/TrEMBL  Length:108

    Alignment length:109
                              1                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98         
         A2NI60_HUMAN     - --DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
               SCOP domains d2q1eb_ B: automated matches                                                                                  SCOP domains
               CATH domains 2q1eB00 B:-1-107 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeee.....eeeeeee.......eeeeee.........ee...ee.......eeee....eeeeee...hhhhheeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2q1e B  -1 ATDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYHCQQYDNLPYTFGQGTKLEIK 107
                                     8        18        28        38        48        58        68        78        88        98         


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with A2NI60_HUMAN | A2NI60 from UniProtKB/TrEMBL  Length:108

    Alignment length:109
                              1                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98         
         A2NI60_HUMAN     - --DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
               SCOP domains d2q1ec_ C: automated matches                                                                                  SCOP domains
               CATH domains 2q1eC00 C:-1-107 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2q1e C  -1 ATDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYHCQQYDNLPYTFGQGTKLEIK 107
                                     8        18        28        38        48        58        68        78        88        98         


Chain D from PDB  Type:PROTEIN  Length:109
 aligned with A2NI60_HUMAN | A2NI60 from UniProtKB/TrEMBL  Length:108

    Alignment length:109
                              1                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98         
         A2NI60_HUMAN     - --DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
               SCOP domains d2q1ed_ D: automated matches                                                                                  SCOP domains
               CATH domains 2q1eD00 D:-1-107 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2q1e D  -1 ATDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYHCQQYDNLPYTFGQGTKLEIK 107
                                     8        18        28        38        48        58        68        78        88        98
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q1E)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2Q1E)

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