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(-) Description

Title :  STRUCTURE OF THE CORE ECTODOMAIN OF THE HEPATITIS C VIRUS ENVELOPE GLYCOPROTEIN 2
 
Authors :  A. G. Khan, J. Whidby, M. T. Miller, H. Scarborough, A. V. Zatorski, A. Cy A. A. Price, S. A. Yost, C. D. Bohannon, J. Jacob, A. Grakoui, J. Marcotr
Date :  09 Sep 14  (Deposition) - 17 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  E,H,L
Biol. Unit 1:  E  (1x)
Biol. Unit 2:  H,L  (1x)
Keywords :  Hepatitis C Virus, E2, Igg-Like Fold, Scavenger Receptor Class B Type I (Sr-Bi), Cd81, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Khan, J. Whidby, M. T. Miller, H. Scarborough, A. V. Zatorski, A. Cygan, A. A. Price, S. A. Yost, C. D. Bohannon, J. Jacob, A. Grakoui, J. Marcotrigiano
Structure Of The Core Ectodomain Of The Hepatitis C Virus Envelope Glycoprotein 2.
Nature V. 509 381 2014
PubMed-ID: 24553139  |  Reference-DOI: 10.1038/NATURE13117

(-) Compounds

Molecule 1 - HEPATITIS C VIRUS ENVELOPE GLYCOPROTEIN 2
    Chains: E
    Engineered: YES
    Expression System: LENTIVIRUS
    Expression System Taxid: 11646
    Fragment: UNP RESIDUES 456-655
    Organism Scientific: HEPATITIS C VIRUS SUBTYPE 2A
    Organism Taxid: 31649
 
Molecule 2 - MOUSE FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: LENTIVIRUS
    Expression System Taxid: 11646
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - MOUSE FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: LENTIVIRUS
    Expression System Taxid: 11646
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : EHL
Biological Unit 1 (1x): E  
Biological Unit 2 (1x):  HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ARF6Ligand/IonFORMAMIDE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ARF1Ligand/IonFORMAMIDE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1ARF5Ligand/IonFORMAMIDE
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG E:634 , GLU E:641 , HOH E:805 , HOH E:812 , SER H:107binding site for residue ARF E 703
2AC2SOFTWAREHIS H:169 , ASP L:173 , HOH L:431binding site for residue ARF H 501
3AC3SOFTWARESER H:113 , THR H:115binding site for residue ARF H 502
4AC4SOFTWAREARG E:634 , ASP H:100 , SER H:102 , TYR L:55binding site for residue ARF H 503
5AC5SOFTWAREGLU H:42 , ASP L:91 , LYS L:109 , ASP L:171 , HOH L:428binding site for residue ARF L 301
6AC6SOFTWAREGLN L:43 , LYS L:45 , LYS L:51 , ASP L:88binding site for residue ARF L 302
7AC7SOFTWAREASN E:558 , SER E:559 , SER E:560 , TYR E:562 , ASP L:190binding site for Mono-Saccharide NAG E 701 bound to ASN E 558
8AC8SOFTWARECYS E:624 , TYR E:628 , ASN E:649binding site for Mono-Saccharide NAG E 702 bound to ASN E 649

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1E:488 -E:624
2E:496 -E:566
3E:510 -E:554
4E:571 -E:601
5E:611 -E:648
6H:22 -H:96
7H:145 -H:200
8L:23 -L:94
9L:140 -L:200

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Cys E:488 -Trp E:489
2Thr E:512 -Pro E:513
3Phe H:151 -Pro H:152
4Glu H:153 -Pro H:154
5Val H:174 -Leu H:175
6Leu H:175 -Gln H:176
7Ser H:177 -Asp H:178
8Trp H:193 -Pro H:194
9Ser L:7 -Pro L:8
10Thr L:100 -Pro L:101
11Tyr L:146 -Pro L:147
12Asn L:196 -Ser L:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WEB)

(-) 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 E from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeee...eeee...................eeeee.....eeeee.....hhhhh..........ee...hhhhhhhhhh...eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4web E 488 CWHYPPRQCGVVSAKTVCGPVYCFTPSPVVVGTTDVFLLNSTRPPLGSWFGCTWMNSSGYTKTCGAPPCTTYLKCGSGPWLTPRCLIDYPYRLWHYPCTVNYTIFKIRMYVGGVEHRLTAACN 649
                                   497       507       517    || 542       552       562       596       606       616       626       636       646   
                                                            522|                              571|                                                     
                                                             538                               596                                                     


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee.........eeeeeeeeee.....eeee........eeeeeee.....eeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4web H   1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYIHWVNQRPEQGLEWIGRIDPANGHTQYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCATSDYSYALDSWGQGTSVTVSSAKTTAPSVYPLAPVCTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   142       152       162       172       182       192       202       212      
                                                                                                                                                              133|                                                                                  
                                                                                                                                                               136                                                                                  


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4web L   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLNSNNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 ; only for superseded entry 4NX3: 1,2)

(no "SCOP Domain" information available for 4WEB, only for superseded entry 4NX3 replaced by 4WEB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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