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(-) Description

Title :  CERATOTOXIN VARIANT IN COMPLEX WITH SPECIFIC ANTIBODY FAB FRAGMENT
 
Authors :  P. Strop, A. Shcherbatko, A. Rossi
Date :  11 Nov 15  (Deposition) - 04 May 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Ceratotoxin, Random Mutagenesis, Nav1. 7 Ion Chanel, Toxin-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shcherbatko, A. Rossi, D. Foletti, G. Zhu, O. Bogin, M. Galindo Casas, M. Rickert, A. Hasa-Moreno, V. Bartsevich, A. Crameri, A. R. Steiner, R. Henningsen, A. Gill, J. Pons, D. L. Shelton, A. Rajpal, P. Strop
Engineering Highly Potent And Selective Microproteins Against Nav1. 7 Sodium Channel For Treatment Of Pain.
J. Biol. Chem. V. 291 13974 2016
PubMed-ID: 27129258  |  Reference-DOI: 10.1074/JBC.M116.725978

(-) Compounds

Molecule 1 - ANTIBODY FAB FRAGMENT HEAVY CHAIN
    Chains: A, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTIBODY FAB FRAGMENT LIGHT CHAIN
    Chains: B, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - BETA-THERAPHOTOXIN-CM1A
    Chains: C, D
    Engineered: YES
    Organism Common: STRAIGHTHORNED BABOON TARANTULA
    Organism Scientific: CERATOGYRUS MARSHALLI
    Organism Taxid: 316287
    Synonym: BETA-TRTX-CM1A,CCOTX1,CERATOTOXIN-1
    Synthetic: YES

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 5EPM)

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:146 -A:201
3B:23 -B:93
4B:139 -B:199
5C:2 -C:17
6C:9 -C:22
7C:16 -C:29
8D:2 -D:17
9D:9 -D:22
10D:16 -D:29
11E:22 -E:96
12E:146 -E:201
13F:23 -F:93
14F:139 -F:199

(-) Cis Peptide Bonds  (12, 13)

Asymmetric Unit
No.Residues
1Phe A:152 -Pro A:153
2Glu A:154 -Pro A:155
3Trp A:194 -Pro A:195
4Thr B:7 -Pro B:8
5Val B:99 -Pro B:100
6Tyr B:145 -Pro B:146
7Phe E:152 -Pro E:153
8Glu E:154 -Pro E:155
9Trp E:194 -Pro E:195
10Thr F:7 -Pro F:8
11Val F:99 -Pro F:100
12Tyr F:145 -Pro F:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EPM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EPM)

(-) Exons   (0, 0)

(no "Exon" information available for 5EPM)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5epm A   1 xVQLQQPGAELLRPGASVKLSCKASGYTFTNFWMNWVKQRPGQGLELIGMIDPSDSETHYNQMFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARRDYYGILFDYWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 219
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                            |                                                                                                                                                                                                                          
                            1-PCA                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5epm B   1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHNNGNTYIEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain C from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.....eee......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 5epm C   1 DCLGMFKSCDPENDKCCKRLVCSRSHRWCKWKL  33
                                    10        20        30   


Chain D from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.....eee......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 5epm D   1 DCLGMFKSCDPENDKCCKRLVCSRSHRWCKWKL  33
                                    10        20        30   


Chain E from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5epm E   1 xVQLQQPGAELLRPGASVKLSCKASGYTFTNFWMNWVKQRPGQGLELIGMIDPSDSETHYNQMFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARRDYYGILFDYWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 219
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                            1-PCA                                                                                                                                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5epm F   1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHNNGNTYIEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 5EPM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EPM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EPM)

(-) Gene Ontology  (5, 5)

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  Cis Peptide Bonds
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    Phe A:152 - Pro A:153   [ RasMol ]  
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