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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF BROADLY NEUTRALIZING HUMAN ANTI - HEPATITIS C VIRUS (HCV) GLYCOPROTEIN E2 FAB FRAGMENT HC84-1
 
Authors :  T. Krey, F. A. Rey
Date :  03 Apr 13  (Deposition) - 05 Jun 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D,I,K,P
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  I,K,P  (1x)
Keywords :  Fab Fragment, Immunglobulin Fold, Antibody, Immune System, Viral Protein-Immune System Complex, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Krey, A. Meola, Z. Y. Keck, L. Damier-Piolle, S. K. Foung, F. A. Rey
Structural Basis Of Hcv Neutralization By Human Monoclonal Antibodies Resistant To Viral Neutralization Escape.
Plos Pathog. V. 9 03364 2013
PubMed-ID: 23696737  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003364

(-) Compounds

Molecule 1 - ANTI-HCV E2 FAB HC84-1 HEAVY CHAIN
    Chains: A, C, I
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Plasmid: PMT FAB
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTI-HCV E2 FAB HC84-1 LIGHT CHAIN
    Chains: B, D, P
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Plasmid: PMT FAB
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ENVELOPE GLYCOPROTEIN E2
    Chains: K
    Engineered: YES
    Fragment: RESIDUES 434-446 OF HCV STRAIN H77 POLYPROTEIN
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS (ISOLATE H)
    Organism Taxid: 11108
    Synonym: NS1, GP68, GP70, GENOME POLYPROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDIKP
Biological Unit 1 (1x): AB     
Biological Unit 2 (1x):   CD   
Biological Unit 3 (1x):     IKP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR K:443 , HIS K:445 , LYS P:30 , ASP P:91 , SER P:92BINDING SITE FOR RESIDUE SO4 K 501
2AC2SOFTWAREGLY I:50 , ILE I:52 , PHE I:55 , THR I:57 , MET I:59 , LEU I:101 , SER I:102 , GLY I:104 , SO4 K:501 , HOH K:601 , HOH K:602 , GLY P:28 , SER P:29 , LYS P:30 , SER P:31 , ASP P:50 , ASN P:65 , TRP P:90 , SER P:92 , SER P:93BINDING SITE FOR CHAIN K OF ENVELOPE GLYCOPROTEIN E2

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:146 -A:202
3B:22 -B:87
4B:133 -B:193
5C:22 -C:96
6C:146 -C:202
7D:22 -D:87
8D:133 -D:193
9I:22 -I:96
10I:146 -I:202
11P:22 -P:87
12P:133 -P:193

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Phe A:152 -Pro A:153
2Glu A:154 -Pro A:155
3Tyr B:139 -Pro B:140
4Phe C:152 -Pro C:153
5Glu C:154 -Pro C:155
6Tyr D:139 -Pro D:140
7Phe I:152 -Pro I:153
8Glu I:154 -Pro I:155
9Tyr P:139 -Pro P:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZN)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee.....eeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzn A   1 QVQLVQSGAEVKKPGSSVKVSCEASGGTYVITWVRQAPGQGLEWMGGFIPTFRTAMYAQGFQGRVTITADESTSIAYMELTNLRSEDTAVYYCARGPLSRGYYDYWGQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKS 221
                                    10        20       |33        43        53        63        73        83        93       103       113       123       139       149       159       169       179       189       199       209       219  
                                                      28|                                                                                                 132|                                                                                  
                                                       32                                                                                                  139                                                                                  


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzn B   1 SYVLTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSVVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 213
                                    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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eee.....eeeeee.eeeeeee......eeeeeee....eeee.......eee..eeee...hhhhheeeeeeee........ee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzn C   2 VQLVQSGAEVKKPGSSVKVSCEYVITWVRQAPGQGLEWMGGFIPTFRTAMYAQGFQGRVTITAYMELTNLRSEDTAVYYCARGPLSRGYYDYWGQGTLVTVSSASTKGPSVFPLAPSSKGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC 222
                                    11        21 ||     39        49        59        69 ||     86        96       106       116       126       139       149       159       169       179       189       199       209       219   
                                                23|                                     71|                                                     135|                                                                                   
                                                 32                                      79                                                      139                                                                                   


Chain D from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzn D   1 SYVLTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSVVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain I from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee......eeeeeeee......eeeeeee....eeee.......eeeee.....eeeeee...hhhhheeeeeeeee.......ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzn I   1 QVQLVQSGAEVKKPGSSVKVSCEASGGTLSNYVITWVRQAPGQGLEWMGGFIPTFRTAMYAQGFQGRVTITADESTSIAYMELTNLRSEDTAVYYCARGPLSRGYYDYWGQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKS 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    146       156       166       176       186       196       206       216     
                                                                                                                                                             132|                                                                                  
                                                                                                                                                              139                                                                                  


Chain K from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4jzn K 435 TGWLAGLFYQHK 446
                                   444  


Chain P from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzn P   0 SSYVLTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSVVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 212
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4JZN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (143, 143)

Asymmetric Unit(hide GO term definitions)

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  4jzn
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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 4jzo 4mwf 4n0y 4q0x 4xvj 4z0x 5eoc 5erw 5fgb 5fgc

(-) Related Entries Specified in the PDB File

4jzo