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(-) Description

Title :  TERNARY COMPLEX AMONG TWO HUMAN DERIVED SINGLE CHAIN ANTIBODY FRAGMENTS AND CN2 TOXIN FROM SCORPION CENTRUROIDES NOXIUS.
 
Authors :  L. Riano-Umbarila, H. Serrano-Posada, S. Rojas-Trejo, E. Rudino-Pin B. Becerril
Date :  25 Sep 14  (Deposition) - 07 Oct 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Toxin-Immune System Complex, Human Scfv, Scorpion Venom Neutralization, Directed Evolution, Cn2 Toxin. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Riano-Umbarila, L. M. Ledezma-Candanoza, H. Serrano-Posada, G. Fernandez-Taboada, T. Olamendi-Portugal, S. Rojas-Trejo, I. V. Gomez-Ramirez, E. Rudino-Pinera, L. D. Possani, B. Becerril
Optimal Neutralization Of Centruroides Noxius Venom Is Understood Through A Structural Complex Between Two Antibody Fragments And The Cn2 Toxin.
J. Biol. Chem. V. 291 1619 2016
PubMed-ID: 26589800  |  Reference-DOI: 10.1074/JBC.M115.685297

(-) Compounds

Molecule 1 - SINGLE CHAIN ANTIBODY FRAGMENT LR, HEAVY CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSYN1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: TG1
    Expression System Vector: PSYN
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SINGLE CHAIN ANTIBODY FRAGMENT LR, LIGHT CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSYN1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: TG1
    Expression System Vector: PSYN
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - BETA-MAMMAL TOXIN CN2
    Chains: C
    Fragment: UNP RESIDUES 17-82
    Organism Common: MEXICAN SCORPION
    Organism Scientific: CENTRUROIDES NOXIUS
    Organism Taxid: 6878
    Synonym: TOXIN 2, TOXIN II.9.2.2
 
Molecule 4 - SINGLE CHAIN ANTIBODY FRAGMENT RU1, HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSYN1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: TG1
    Expression System Vector: PSYN
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - SINGLE CHAIN ANTIBODY FRAGMENT RU1, LIGHT CHAIN
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSYN1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: TG1
    Expression System Vector: PSYN
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4V1D)

(-) Sites  (0, 0)

(no "Site" information available for 4V1D)

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2B:155 -B:220
3C:12 -C:65
4C:16 -C:41
5C:25 -C:46
6C:29 -C:48
7D:22 -D:96
8D:103 -D:106
9E:161 -E:228

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser B:139 -Pro B:140
2Ser B:226 -Pro B:227
3Trp C:58 -Pro C:59
4Ser E:190 -His E:191
5Asn E:192 -Gln E:193
6Ser E:234 -Leu E:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V1D)

(-) Exons   (0, 0)

(no "Exon" information available for 4V1D)

(-) Sequences/Alignments

Asymmetric/Biological 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:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhh.eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4v1d A   1 EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGFGSFDTWGQGTMVTVSS 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eee......eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4v1d B 132 SEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEIKR 240
                                   141       151       161       171       181       191       201       211       221       231         


Chain C from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee...............eehhhhhhhhhhhhh...eeeee..eeeee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 4v1d C   1 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS  66
                                    10        20        30        40        50        60      


Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...........eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v1d D   1 QVNLRESGGGLVQPGGSLRLSCAASGFSFGSYGMHWVRQAPGKGLEWVAVISYGGGNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDARDCLLCADWHFDLWGRGTLVTVSS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain E from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4v1d E 139 SNFMLTQPHSASGTPGQRVTISCSGSSSNIGSNTVNWYRHLPGSAPELLIGSHNQRPSGVPDRFSASKSDTSASLAISGLQSEDEADYYCAAWDDSLIGYVFGTGTKLTVLG 250
                                   148       158       168       178       188       198       208       218       228       238       248
   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 4V1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V1D)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4v1d)
 
  Cis Peptide Bonds
    Asn E:192 - Gln E:193   [ RasMol ]  
    Ser B:139 - Pro B:140   [ RasMol ]  
    Ser B:226 - Pro B:227   [ RasMol ]  
    Ser E:190 - His E:191   [ RasMol ]  
    Ser E:234 - Leu E:235   [ RasMol ]  
    Trp C:58 - Pro C:59   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCX2_CENNO | P01495: 1cn2 2ybr 2yc1

(-) Related Entries Specified in the PDB File

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