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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF BROADLY NEUTRALIZING HUMAN ANTI - HEPATITIS C VIRUS (HCV) GLYCOPROTEIN E2 FAB FRAGMENT HC33.8
 
Authors :  C. Girard-Blanc, F. A. Rey, T. Krey
Date :  20 Dec 15  (Deposition) - 20 Jan 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,E
Keywords :  Fab Fragment, Neutralizing Antibody, Hepatitis C Virus E2, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Y. Keck, C. Girard-Blanc, W. Wang, P. Lau, A. Zuiani, F. A. Rey, T. Krey, M. S. Diamond, S. K. Foung
Antibody Response To Hypervariable Region 1 Interferes With Broadly Neutralizing Antibodies To Hepatitis C Virus.
J. Virol. V. 90 3112 2016
PubMed-ID: 26739044  |  Reference-DOI: 10.1128/JVI.02458-15

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A
    EC Number: 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
    Engineered: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS GENOTYPE 1A (ISOLATE H)
    Organism Taxid: 11108
    Synthetic: YES
 
Molecule 2 - ANTI-HCV E2 FAB HC33.8 LIGHT CHAIN
    Chains: B
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Cell Line: SCHNEIDER 2
    Expression System Plasmid: PMT/BIP MODIFIED
    Expression System Taxid: 7215
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTI-HCV E2 FAB HC33.8 HEAVY CHAIN
    Chains: E
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Cell Line: SCHNEIDER 2
    Expression System Plasmid: PMT/BIP MODIFIED
    Expression System Taxid: 7215
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5FGC)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1B:22 -B:87
2B:134 -B:194
3B:214 -E:230
4E:22 -E:96
5E:154 -E:210

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr B:140 -Pro B:141
2Phe E:160 -Pro E:161
3Glu E:162 -Pro E:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FGC)

(-) Sequences/Alignments

Asymmetric/Biological 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:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5fgc A 415 NTNGSWHIN 423


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee...eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgc B   1 SYELTQPPSVSVSPGQAATITCSGDKLGDKYVSWYQQRPGQSPLLVVYQDNKRPSGIPERISGSNSGNTATLTIRGTRAMDEADYYCQAWDSSTDVVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain E from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeee..........eeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgc E   1 EVQLVESGGGLAQPGESLRLSCAASGFNFYTYAMTWVRQAPGKGLEWVSASSSTDGTTYYADSVKGRFTISRDNSKNILYLQMNSLKAEDTATYYCARAVVFTDSSAYYYSKYFDYWSQGTLVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140||     155       165       175       185       195       205       215       225     
                                                                                                                                                                      141|                                                                                   
                                                                                                                                                                       147
   Legend:   → Mismatch (orange background)
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    → 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 5FGC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (143, 143)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5fgc)
 
  Cis Peptide Bonds
    Glu E:162 - Pro E:163   [ RasMol ]  
    Phe E:160 - Pro E:161   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        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 5eoc 5erw 5fgb

(-) Related Entries Specified in the PDB File

5fgb 5FGB CONTAINS A RELATED FAB FRAGMENT CRYSTALLIZED WITH THE SAME PEPTIDE