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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AMYLOID-FORMING IMMUNOGLOBULIN AL-103 CIS-PROLINE 95 MUTANT
 
Authors :  J. R. Thompson, D. S. Berkholz, E. W. Mahlum, M. Ramirez-Alvarado
Date :  03 Apr 13  (Deposition) - 30 Oct 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Biol. Unit 5:  I,J  (1x)
Keywords :  Immunoglobulin Variable Domain, Amyloid Protein, Patient-Derived Sequence, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Blancas-Mejia, A. Tischer, J. R. Thompson, J. Tai, L. Wang, M. Auton, M. Ramirez-Alvarado
Kinetic Control In Protein Folding For Light Chain Amyloidosis And The Differential Effects Of Somatic Mutations.
J. Mol. Biol. V. 426 347 2014
PubMed-ID: 24157440  |  Reference-DOI: 10.1016/J.JMB.2013.10.016

(-) Compounds

Molecule 1 - AMYLOIDOGENIC IMMUNOGLOBULIN LIGHT CHAIN PROTEIN AL-103
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VARIABLE DOMAIN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): AB        
Biological Unit 2 (1x):   CD      
Biological Unit 3 (1x):     EF    
Biological Unit 4 (1x):       GH  
Biological Unit 5 (1x):         IJ

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
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:27 , ASP B:28 , SER F:65 , GLY F:66BINDING SITE FOR RESIDUE SO4 B 201

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:88
2B:23 -B:88
3C:23 -C:88
4D:23 -D:88
5E:23 -E:88
6F:23 -F:88
7G:23 -G:88
8H:23 -H:88
9I:23 -I:88
10J:23 -J:88

(-) Cis Peptide Bonds  (20, 20)

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
9Ser E:7 -Pro E:8
10Leu E:94 -Pro E:95
11Ser F:7 -Pro F:8
12Leu F:94 -Pro F:95
13Ser G:7 -Pro G:8
14Leu G:94 -Pro G:95
15Ser H:7 -Pro H:8
16Leu H:94 -Pro H:95
17Ser I:7 -Pro I:8
18Leu I:94 -Pro I:95
19Ser J:7 -Pro J:8
20Leu J:94 -Pro J:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K07)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K07)

(-) Exons   (0, 0)

(no "Exon" information available for 4K07)

(-) 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:108
                                                                                                                                            
               SCOP domains d4k07a_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 A   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07b_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4k07 B   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain C from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07c_ C: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 C   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain D from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07d_ D: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 D   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain E from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07e_ E: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 E   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain F from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07f_ F: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 F   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain G from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07g_ G: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 G   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain H from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07h_ H: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 H   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain I from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07i_ I: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 I   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99        


Chain J from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4k07j_ J: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ 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
                 4k07 J   0 TDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTFGPGTKLEIK 107
                                     9        19        29        39        49        59        69        79        89        99
   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, 10)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K07)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K07)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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        KV133_HUMAN | P01594: 1b0w 1jv5 1qp1 2q20 3cdc 3cdf 3cdy

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