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(-) Description

Title :  STRUCTURE OF PHAGE TP901-1 RBP (ORF49) IN COMPLEX WITH NANOBODY 11.
 
Authors :  A. Desmyter, C. Farenc, J. Mahony, S. Spinelli, C. Bebeacua, S. Blangy, D. Veesler, D. Van Sinderen, C. Cambillau
Date :  08 Jan 13  (Deposition) - 20 Mar 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,E,F,G  (1x)
Biol. Unit 2:  D,H  (3x)
Keywords :  All Beta, Jelly Roll Motif, Receptor Binding Protein, Neutralizing Llama Antibody Domain, Cell Adhesion-Immune System Complex, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Desmyter, C. Farenc, J. Mahony, S. Spinelli, C. Bebeacua, S. Blangy D. Veesler, D. Van Sinderen, C. Cambillau
Viral Infection Modulation And Neutralization By Camelid Nanobodies
Proc. Natl. Acad. Sci. Usa V. 110 E1371 2013
PubMed-ID: 23530214  |  Reference-DOI: 10.1073/PNAS.1301336110

(-) Compounds

Molecule 1 - BPP
    Chains: A, B, C, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PET20G
    Fragment: HEAD DOMAIN, RESIDUES 64-163
    Gene: BPP, ORF49
    Organism Scientific: LACTOCOCCUS PHAGE TP901-1
    Organism Taxid: 35345
    Synonym: BASEPLATE PROTEIN
 
Molecule 2 - LLAMA NANOBODY 11
    Chains: D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABC EFG 
Biological Unit 2 (3x):    D   H

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:106 , ARG B:107 , SER B:108 , TRP C:67 , ARG C:107 , SER C:108BINDING SITE FOR RESIDUE GOL B 201

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1D:22 -D:96
2E:22 -E:96
3F:22 -F:96
4G:22 -G:96

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Trp D:102 -Gly D:103
2Asn E:74 -Ala E:75
3Ala E:75 -Lys E:76
4Trp E:102 -Gly E:103
5Trp F:102 -Gly F:103
6Gly G:26 -Arg G:27
7Ala G:75 -Lys G:76
8Trp G:102 -Gly G:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IOS)

(-) 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:100
                                                                                                                                    
               SCOP domains d4iosa_ A: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee..eeeeeeee.................hhhhh....eeeeeee.....eeeeee......ee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4ios A  64 TKSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID 163
                                    73        83        93       103       113       123       133       143       153       163


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains d4iosb_ B: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee..eeeeeeee.................hhhhh....eeeeeee.....eeeeee......ee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4ios B  65 KSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID 163
                                    74        84        94       104       114       124       134       144       154         


Chain C from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains d4iosc_ C: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee..eeeeeeee.................hhhhh....eeeeeee.....eeeeee......ee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4ios C  65 KSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID 163
                                    74        84        94       104       114       124       134       144       154         


Chain D from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d4iosd_ D: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..eeeeeee......eeeeeee.....eee.......eeeee..eeeeee........eeeeeeee......hhhhh.ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4ios D   2 VQLVESGGGLVQAGDSLRLSCAVSSNVIGWFRQAPGKEREFVAAISWSTGSTYYGRSMKGRCAASRDNTVALQLNSLKPEDTAVYYCAATLDWGKTLSDEYDYWGQGTQVTVS 122
                                    11        21   ||   36        46        56        66      ||79        89        99       109       119   
                                                  25|                                        73|                                             
                                                   31                                         77                                             


Chain E from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains d4iose_ E: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eee....eeeeeeee....eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee........eeeeeeee......hhhhh.ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4ios E   2 VQLVESGGGLVQAGDSLRLSCAVSGRSNVIGWFRQAPGKEREFVAAISWSTGSTYYGRSMKGRCAASRDNAKNTVALQLNSLKPEDTAVYYCAATLDWGKTLSDEYDYWGQGTQVTVS 122
                                    11        21     || 34        44        54        64        74        84        94       104       114        
                                                    27|                                                                                           
                                                     31                                                                                           


Chain F from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains d4iosf_ F: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee...eeeeeee......eeeeeee.....eee.......eeeee...eeeeee........eeeeeeee......hhhhh.ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4ios F   2 VQLVESGGGLVQAGDSLRLSCAVSGSNVIGWFRQAPGKEREFVAAISWSTGSTYYGRSMKGRCAASRDKNTVALQLNSLKPEDTAVYYCAATLDWGKTLSDEYDYWGQGTQVTVS 122
                                    11        21    ||  35        45        55        65       |77        87        97       107       117     
                                                   26|                                        73|                                              
                                                    31                                         76                                              


Chain G from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d4iosg_ G: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eeeeeeee....eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee........eeeeeeee......hhhhh.ee...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4ios G   2 VQLVESGGGLVQAGDSLRLSCAVSGRSNVIGWFRQAPGKEREFVAAISWSTGSTYYGRSMKGRCAASRDNAKNTVALQLNSLKPEDTAVYYCAATLDWGKTLSDEYDYWGQGTQVTV 121
                                    11        21     || 34        44        54        64        74        84        94       104       114       
                                                    27|                                                                                          
                                                     31                                                                                          


Chain H from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains d4iosh_ H: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee..eeeeeeee.................hhhhh....eeeeeee.....eeeeee......ee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4ios H  64 TKSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID 163
                                    73        83        93       103       113       123       133       143       153       163
   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  (2, 8)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        Q9G096_9CAUD | Q9G096: 2f0c 3d8m 3da0 3ejc 3hg0 3u6x 4hem 4hep 4v96

(-) Related Entries Specified in the PDB File

4hem 4hep