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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF BROADLY NEUTRALIZING HUMAN ANTI - HEPATITIS C VIRUS (HCV) GLYCOPROTEIN E2 FAB FRAGMENT HC33.4
 
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 :  1.65
Chains :  Asym. Unit :  A,B,C,E,F,G
Biol. Unit 1:  A,C,F  (1x)
Biol. Unit 2:  B,E,G  (1x)
Keywords :  Fab Fragment, Neutralizing Antibody, Hepatitis C Virus E2, Immune System (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 - ANTI-HCV E2 FAB HC84-1 LIGHT CHAIN
    Chains: A, 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 2 - ANTI-HCV E2 FAB HC84-1 HEAVY CHAIN
    Chains: C, 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
 
Molecule 3 - GENOME POLYPROTEIN
    Chains: F, G
    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
    Other Details: FRAGMENT RESIDUES 406-425 OF HCV STRAIN H77 POLYPROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCEFG
Biological Unit 1 (1x): A C F 
Biological Unit 2 (1x):  B E G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:162 , SER A:176 , SER A:177 , THR A:178 , HOH A:433 , PHE C:175 , PRO C:176 , VAL C:178 , SER C:186 , LEU C:187 , SER C:188binding site for residue GOL A 301
02AC2SOFTWAREARG A:211binding site for residue SO4 A 302
03AC3SOFTWARETHR A:109 , VAL A:110 , HOH A:409binding site for residue SO4 A 303
04AC4SOFTWARESER A:156 , GLY A:157 , SER A:159 , HOH A:401 , HOH A:445 , HOH A:470 , HOH A:527binding site for residue SO4 A 304
05AC5SOFTWARESER B:162 , SER B:176 , SER B:177 , THR B:178 , HOH B:603 , PHE E:175 , PRO E:176 , VAL E:178 , SER E:186 , LEU E:187 , SER E:188binding site for residue GOL B 301
06AC6SOFTWAREARG B:211binding site for residue SO4 B 302
07AC7SOFTWARESER B:156 , GLY B:157 , HOH B:612 , HOH B:624 , HOH B:651binding site for residue SO4 B 303
08AC8SOFTWARESER C:54 , ARG C:72 , ASP C:73 , ASN C:74binding site for residue GOL C 301
09AC9SOFTWARESER C:52 , SER C:54 , GLY C:56 , SER C:57 , HOH C:426 , HOH C:472 , SER F:419binding site for residue SO4 C 302
10AD1SOFTWARETYR C:59 , HOH C:410 , HOH C:453 , HIS F:421binding site for residue SO4 C 303
11AD2SOFTWAREGLY E:10 , THR E:116 , LEU E:117 , PRO E:158binding site for residue GOL E 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:87
2A:134 -A:194
3B:22 -B:87
4B:134 -B:194
5C:22 -C:96
6C:149 -C:205
7E:22 -E:96
8E:149 -E:205

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:140 -Pro A:141
2Tyr B:140 -Pro B:141
3Phe C:155 -Pro C:156
4Glu C:157 -Pro C:158
5Phe E:155 -Pro E:156
6Glu E:157 -Pro E:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FGB)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgb A   1 SYELTQLPSLSVSLGQTASITCSGDNLGDKFVCWYQQKPGQTPVLVMYEDTKRPSGIPERFAGSNSGNTATLTITGTQAMDEADYYCQTWDSSTDVVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeeee.........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgb B   1 SYELTQLPSLSVSLGQTASITCSGDNLGDKFVCWYQQKPGQTPVLVMYEDTKRPSGIPERFAGSNSGNTATLTITGTQAMDEADYYCQTWDSSTDVVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgb C   1 EVQLVQSGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNILYLQMNSLKAEDTATYYCARAVVFYYSKYFDYWSQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPK 223
                                    10        20        30        40        50        60        70        80        90       100 ||    111       121       131   ||  148       158       168       178       188       198       208       218     
                                                                                                                               102|                            135|                                                                                
                                                                                                                                104                             143                                                                                


Chain E from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgb E   1 EVQLVQSGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNILYLQMNSLKAEDTATYYCARAVVFSKYFDYWSQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEP 222
                                    10        20        30        40        50        60        70        80        90       100 ||    113       123       133 ||    149       159       169       179       189       199       209       219   
                                                                                                                               102|                          135|                                                                                
                                                                                                                                106                           142                                                                                


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5fgb F 417 NGSWH 421


Chain G from PDB  Type:PROTEIN  Length:4
                                    
               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
                 5fgb G 418 GSWH 421
   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 5FGB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (143, 143)

Asymmetric Unit(hide GO term definitions)

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  5fgb
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  POLG_HCVH | P27958
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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 5fgc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FGB)