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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB C2 IN COMPLEX WITH A CYCLIC VARIANT OF HEPATITIS C VIRUS E2 EPITOPE I
 
Authors :  R. Berisio, A. Ruggiero, A. Sandomenico, A. H. Patel, M. Ruvo, L. Vitagl
Date :  10 Nov 15  (Deposition) - 10 Feb 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  H,J,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  J,M,Q  (1x)
Keywords :  Complex, Monoclonal Antibodies, Hcv, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sandomenico, A. Leonardi, R. Berisio, L. Sanguigno, G. Foca, A. Foca, A. Ruggiero, N. Doti, L. Muscariello, D. Barone, C. Farina, A. Owsianka, L. Vitagliano, A. H. Patel, M. Ruvo
Generation And Characterization Of Monoclonal Antibodies Against A Cyclic Variant Of Hepatitis C Virus E2 Epitope 412-422.
J. Virol. V. 90 3745 2016
PubMed-ID: 26819303  |  Reference-DOI: 10.1128/JVI.02397-15

(-) Compounds

Molecule 1 - FAB FRAGMENT (HEAVY CHAIN)
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FAB FRAGMENT (LIGHT CHAIN)
    Chains: L, M
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - FAB FRAGMENT (HEAVY CHAIN)
    Chains: J
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 4 - ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS
    Chains: P, Q
    Engineered: YES
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 11103
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HJLMPQ
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  J M Q

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5EOC)

(-) Sites  (0, 0)

(no "Site" information available for 5EOC)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:144 -H:199
3J:22 -J:96
4J:144 -J:199
5L:23 -L:92
6L:138 -L:198
7M:23 -M:92
8M:138 -M:198
9P:411 -P:423
10Q:411 -Q:423

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe H:150 -Pro H:151
2Glu H:152 -Pro H:153
3Trp H:192 -Pro H:193
4Ser L:7 -Pro L:8
5Tyr L:144 -Pro L:145
6Phe J:150 -Pro J:151
7Glu J:152 -Pro J:153
8Trp J:192 -Pro J:193
9Ser M:7 -Pro M:8
10Tyr M:53 -Leu M:54
11Leu M:98 -Thr M:99
12Tyr M:144 -Pro M:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EOC)

(-) 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 H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee........eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eoc H   1 EVQLQQPGAELVRPGGSVKLSCKASGYSFTTYWMNWVKQRPGQGLEWIGMIQPSDSETRLNQKFKDKATLTLDRSSSTVYMQLSSPTSDDSAVYYCARTGRGDAWLTYWGQGTSVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    145       155       165       175       185       195       205       215  
                                                                                                                                                             132|                                                                               
                                                                                                                                                              138                                                                               


Chain J from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeee.....eeeeeeee........eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eoc J   2 VQLQQPGAELVRPGGSVKLSCKASGYSFTTYWMMWVKQRPGQGLEWIGMIQPSDSETRLNQKFKDKATLTLDRSSSTVYMQLSSPTSDDSAVYYCARTGRGDAWLTYWGQGTSVTVSSAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  ||   143       153       163       173       183       193       203       213    
                                                                                                                                                              134|                                                                                
                                                                                                                                                               137                                                                                


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5eoc L   1 NIVLTQSPVSLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPRLLLYLGSNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHIRELTRSFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain M from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee...eeeeeeee.........eeeeeeee......eeeeee............eeee...eeeeee..hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eoc M   1 NIVLTQSPVSLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPRLLLYLGSNLESGVPARFSGSGSGTDFTLNIPVEEEDAATYYCQHIRELTRSFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 216
                                    10        20        30        40        50        60        70        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
                                                                                                         79|                                                                                                                                       
                                                                                                          81                                                                                                                                       


Chain P from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5eoc P 411 CQLINTNGSWHIC 423
                                   420   


Chain Q from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5eoc Q 411 CQLINTNGSWHIC 423
                                   420
   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 5EOC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (143, 143)

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  Cis Peptide Bonds
    Glu H:152 - Pro H:153   [ RasMol ]  
    Glu J:152 - Pro J:153   [ RasMol ]  
    Leu M:98 - Thr M:99   [ RasMol ]  
    Phe H:150 - Pro H:151   [ RasMol ]  
    Phe J:150 - Pro J:151   [ RasMol ]  
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    Ser M:7 - Pro M:8   [ RasMol ]  
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    Tyr M:144 - Pro M:145   [ RasMol ]  
    Tyr M:53 - Leu M:54   [ RasMol ]  
 
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        POLG_HCVH | P27958: 1a1r 1a1v 1cwx 1hei 1jr6 1n1l 1onb 1r7c 1r7d 1r7e 1r7f 1r7g 1rgq 2a4r 2f9v 2hd0 2jxf 2kdr 2n1p 2o8m 2obo 2obq 2oc0 2oc1 2oc7 2oc8 2oin 2p59 2qv1 2xi2 2xi3 2xni 4cl1 4jzn 4jzo 4mwf 4n0y 4q0x 4xvj 4z0x 5erw 5fgb 5fgc

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