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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 :  10 Mar 11  (Deposition) - 13 Apr 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (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
    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
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SINGLE CHAIN ANTIBODY FRAGMENT 9004G
    Chains: B, 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
    Fragment: LIGHT CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - BETA-MAMMAL TOXIN CN2
    Chains: C, F
    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

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:160 , ARG B:162 , TYR C:33 , GLY C:34 , LYS C:35 , GOL C:1067 , GOL C:1068BINDING SITE FOR RESIDUE GOL C1066
2AC2SOFTWARESER B:160 , ARG B:162 , ARG B:224 , HOH B:2029 , GOL C:1066BINDING SITE FOR RESIDUE GOL C1067
3AC3SOFTWARESER E:160 , ARG E:162 , ARG E:224 , GOL E:1242 , HOH E:2024 , HOH E:2072BINDING SITE FOR RESIDUE GOL E1240
4AC4SOFTWAREGLN E:169 , LYS E:171 , ARG E:177 , PRO E:191 , GLU E:213 , ASP E:214BINDING SITE FOR RESIDUE GOL E1241
5AC5SOFTWARESER E:160 , ARG E:162 , GOL E:1240 , TYR F:33 , GLY F:34 , LYS F:35 , GOL F:1066BINDING SITE FOR RESIDUE GOL E1242
6AC6SOFTWARETYR C:33 , GLY C:34 , LYS C:35 , GLY C:36 , HIS C:50 , LEU C:51 , TYR C:52 , GOL C:1066BINDING SITE FOR RESIDUE GOL C1068
7AC7SOFTWAREGOL E:1242 , TYR F:33 , GLY F:34 , LYS F:35 , GLY F:36 , ALA F:37 , HIS F:50 , LEU F:51 , TYR F:52BINDING SITE FOR RESIDUE GOL F1066
8AC8SOFTWARESER A:54 , ARG C:27 , SER D:17 , GLN D:82 , HOH D:2108BINDING SITE FOR RESIDUE GOL D1118
9AC9SOFTWARESER A:17 , GLN A:82 , HOH A:2131 , SER D:54 , ARG F:27BINDING SITE FOR RESIDUE GOL A1118

(-) SS Bonds  (12, 12)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser B:139 -Pro B:140
2Ser B:226 -Pro B:227
3Trp C:58 -Pro C:59
4Ser E:139 -Pro E:140
5Ser E:226 -Pro E:227
6Trp F:58 -Pro F:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YC1)

(-) Exons   (0, 0)

(no "Exon" information available for 2YC1)

(-) 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:117
                                                                                                                                                     
               SCOP domains d2yc1a_ A: automated matches                                                                                          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
                 2yc1 A   1 EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTVSS 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d2yc1b_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2yc1 B 132 SEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEIK 239
                                   141       151       161       171       181       191       201       211       221       231        


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 d2yc1c_ 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
                 2yc1 C   1 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC  65
                                    10        20        30        40        50        60     


Chain D from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d2yc1d_ D: automated matches                                                                                          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
                 2yc1 D   1 EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTVSS 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain E from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d2yc1e_ E: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2yc1 E 132 SEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEIK 239
                                   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 d2yc1f_ F: Scorpion toxin                                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
           Pfam domains (1) Toxin_3-2yc1F01 F:1-55                                 ---------- Pfam domains (1)
           Pfam domains (2) Toxin_3-2yc1F02 F:1-55                                 ---------- Pfam domains (2)
         Sec.struct. author ..ee.................hhhhhhhhhhhhh...eeeee..eeeee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2yc1 F   1 KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC  65
                                    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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YC1)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Knottin_1 (78)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain C,F   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        SCX2_CENNO | P01495: 1cn2 2ybr 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
2ybr CRYSTAL STRUCTURE OF THE HUMAN DERIVED SINGLE CHAIN ANTIBODY FRAGMENT (SCFV) 9004G IN COMPLEX WITH CN2 TOXIN FROM THE SCORPION CENTRUROIDES NOXIUS HOFFMANN