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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN DERIVED SINGLE CHAIN ANTIBODY FRAGMENT (SCFV) 9004G IN COMPLEX WITH CN2 TOXIN FROM THE SCORPION CENTRUROIDES NOXIUS HOFFMANN
 
Authors :  J. C. Canul-Tec, L. Riano-Umbarila, E. Rudino-Pinera, B. Becerril, L. D. Possani, A. Torres-Larios
Date :  09 Mar 11  (Deposition) - 13 Apr 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Keywords :  Immune System-Toxin Complex, Scorpion Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Canul-Tec, L. Riano-Umbarila, E. Rudino-Pinera, B. Becerril, L. D. Possani, A. Torres-Larios
Structural Basis Of Neutralization Of The Major Toxic Component From The Scorpion Centruroides Noxius Hoffmann By A Human-Derived Single Chain Antibody Fragment
J. Biol. Chem. V. 286 20892 2011
PubMed-ID: 21489992  |  Reference-DOI: 10.1074/JBC.M111.238410

(-) Compounds

Molecule 1 - SINGLE CHAIN ANTIBODY FRAGMENT 9004G
    Chains: A, D, G
    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
    Fragment: HEAVY CHAIN, RESIDUES 1-117
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SINGLE CHAIN ANTIBODY FRAGMENT 9004G
    Chains: B, E, H
    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
    Fragment: LIGHT CHAIN, RESIDUES 118-263
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - BETA-MAMMAL TOXIN CN2
    Chains: C, F, I
    Organism Common: MEXICAN SCORPION
    Organism Scientific: CENTRUROIDES NOXIUS HOFFMANN
    Organism Taxid: 6878
    Synonym: CN2 TOXIN, TOXIN 2, TOXIN II.9.2.2

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): ABC      
Biological Unit 2 (1x):    DEF   
Biological Unit 3 (1x):       GHI

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2YBR)

(-) SS Bonds  (18, 18)

Asymmetric 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
8E:155 -E:220
9F:12 -F:65
10F:16 -F:41
11F:25 -F:46
12F:29 -F:48
13G:22 -G:96
14H:155 -H:220
15I:12 -I:65
16I:16 -I:41
17I:25 -I:46
18I:29 -I:48

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:116 -Ser A:117
2Ser B:139 -Pro B:140
3Ser B:226 -Pro B:227
4Trp C:58 -Pro C:59
5Ser E:139 -Pro E:140
6Ser E:226 -Pro E:227
7Trp F:58 -Pro F:59
8Ser H:139 -Pro H:140
9Ser H:226 -Pro H:227
10Trp I:58 -Pro I:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YBR)

(-) 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:116
                                                                                                                                                    
               SCOP domains d2ybra_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhh.eee.hhh...eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybr A   2 VQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTVSS 117
                                    11        21        31        41        51        61        71        81        91       101       111      


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains d2ybrb_ B: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2ybr B 128 GGGGSEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEIK 239
                                   137       147       157       167       177       187       197       207       217       227       237  


Chain C from PDB  Type:PROTEIN  Length:65
 aligned with SCX2_CENNO | P01495 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:65
                                    26        36        46        56        66        76     
           SCX2_CENNO    17 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC  81
               SCOP domains d2ybrc_ C: Scorpion toxin                                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.................hhhhhhhhhhhhh...eeeee..eeeee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2ybr C   1 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC  65
                                    10        20        30        40        50        60     


Chain D from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains d2ybrd_ D: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhh.eee.hhh...eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybr D   1 EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTV 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain E from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d2ybre_ E: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eee......eeeeeee.......eeeeee......eeee.............eeeee...eeeeee...hhhhh.eeeeee......ee...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2ybr E 132 SEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEI 238
                                   141       151       161       171       181       191       201       211       221       231       


Chain F from PDB  Type:PROTEIN  Length:65
 aligned with SCX2_CENNO | P01495 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:65
                                    26        36        46        56        66        76     
           SCX2_CENNO    17 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC  81
               SCOP domains d2ybrf_ F: Scorpion toxin                                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.................hhhhhhhhhhhhh...eeeee..eeeee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2ybr F   1 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC  65
                                    10        20        30        40        50        60     


Chain G from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains d2ybrg_ G: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhh.eee.hhh...eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybr G   1 EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTV 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain H from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d2ybrh_ H: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee..eeee.....eeeeeee.......eeeeee......eeeeee..ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2ybr H 127 SGGGGSEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEIKR 240
                                   136       146       156       166       176       186       196       206       216       226       236    


Chain I from PDB  Type:PROTEIN  Length:66
 aligned with SCX2_CENNO | P01495 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:66
                                    26        36        46        56        66        76      
           SCX2_CENNO    17 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS  82
               SCOP domains d2ybri_ I: Scorpion toxin                                          SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
           Pfam domains (1) Toxin_3-2ybrI01 I:1-55                                 ----------- Pfam domains (1)
           Pfam domains (2) Toxin_3-2ybrI02 I:1-55                                 ----------- Pfam domains (2)
           Pfam domains (3) Toxin_3-2ybrI03 I:1-55                                 ----------- Pfam domains (3)
         Sec.struct. author ..ee.................hhhhhhhhhhhhh...eeeee..eeeee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2ybr I   1 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS  66
                                    10        20        30        40        50        60
   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  (3, 9)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Knottin_1 (78)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain C,F,I   (SCX2_CENNO | P01495)
molecular function
    GO:0008200    ion channel inhibitor activity    Stops, prevents, or reduces the activity of an ion channel.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    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.

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  Cis Peptide Bonds
    Ser A:116 - Ser A:117   [ RasMol ]  
    Ser B:139 - Pro B:140   [ RasMol ]  
    Ser B:226 - Pro B:227   [ RasMol ]  
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    Ser E:226 - Pro E:227   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        SCX2_CENNO | P01495: 1cn2 2yc1 4v1d

(-) Related Entries Specified in the PDB File

1cn2 SOLUTION STRUCTURE OF TOXIN 2 FROM CENTRUROIDES NOXIUS HOFFMANN, A BETA SCORPION NEUROTOXIN ACTING ON SODIUM CHANNELS, NMR, 15 STRUCTURES
2yc1 CRYSTAL STRUCTURE OF THE HUMAN DERIVED SINGLE CHAIN ANTIBODY FRAGMENT (SCFV) 9004G IN COMPLEX WITH CN2 TOXIN FROM THE SCORPION CENTRUROIDES NOXIUS HOFFMANN