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(-) Description

Title :  HEPATITIS E VIRUS E2S DOMAIN (GENOTYPE I) IN COMPLEX WITH A NEUTRALIZING ANTIBODY
 
Authors :  X. H. Tang, J. Sivaraman
Date :  18 Apr 11  (Deposition) - 08 Jun 11  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A,H,L  (1x)
Biol. Unit 3:  B,C,D  (1x)
Keywords :  Hepatitis E Virus Capsid Protein, Neutralizing Antibody, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. H. Tang, C. Y. Yang, Y. Gu, C. L. Song, X. Zhang, Y. B. Wang, J. Zhang, C. L. Hew, S. W. Li, N. S. Xia, J. Sivaraman
Structural Basis For The Neutralization And Genotype Specificity Of Hepatitis E Virus
Proc. Natl. Acad. Sci. Usa V. 108 10266 2011
PubMed-ID: 21642534  |  Reference-DOI: 10.1073/PNAS.1101309108

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTO-T7
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 459-603
    Gene: ORF2
    Mutation: YES
    Organism Common: HEV-1
    Organism Scientific: HEPATITIS E VIRUS
    Organism Taxid: 12461
    Synonym: PROTEIN ORF2, PORF2
 
Molecule 2 - MONOCLONAL ANTIBODY, LIGHT CHAIN
    Cell Line: MYELOMA CELL LINE
    Chains: L, C
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: SP2/0 AG15
 
Molecule 3 - MONOCLONAL ANTIBODY, HEAVY CHAIN
    Cell Line: MYELOMA CELL LINE
    Chains: H, D
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: SP2/0 AG15

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x): A (1x)B (1x)    
Biological Unit 2 (1x): A   HL
Biological Unit 3 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3RKD)

(-) Sites  (0, 0)

(no "Site" information available for 3RKD)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1C:23 -C:88
2C:134 -C:194
3D:22 -D:97
4D:151 -D:206
5H:22 -H:97
6H:151 -H:206
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Gly A:591 -Pro A:592
2Gly B:591 -Pro B:592
3Ser L:7 -Pro L:8
4Asn L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Phe H:157 -Pro H:158
7Glu H:159 -Pro H:160
8Trp H:199 -Pro H:200
9Ser C:7 -Pro C:8
10Asn C:94 -Pro C:95
11Tyr C:140 -Pro C:141
12Phe D:157 -Pro D:158
13Glu D:159 -Pro D:160
14Trp D:199 -Pro D:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RKD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RKD)

(-) Exons   (0, 0)

(no "Exon" information available for 3RKD)

(-) 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:146
 aligned with B0VX51_HEV | B0VX51 from UniProtKB/TrEMBL  Length:660

    Alignment length:146
                                   468       478       488       498       508       518       528       538       548       558       568       578       588       598      
           B0VX51_HEV   459 SRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPH 604
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eeeeeeeeeeee..........eeee..eeeee.....eee.hhhhhhh.ee..ee..eeee..eeeeeee.....eeee..................eeeee......eeee..........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd A 459 SRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQHSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPP 604
                                   468       478       488       498       508       518       528       538       548       558       568       578       588       598      


Chain A from PDB  Type:PROTEIN  Length:146
 aligned with CAPSD_HEVPA | P33426 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:146
                                   468       478       488       498       508       518       528       538       548       558       568       578       588       598      
          CAPSD_HEVPA   459 SRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPH 604
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eeeeeeeeeeee..........eeee..eeeee.....eee.hhhhhhh.ee..ee..eeee..eeeeeee.....eeee..................eeeee......eeee..........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd A 459 SRPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQHSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPP 604
                                   468       478       488       498       508       518       528       538       548       558       568       578       588       598      


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with B0VX51_HEV | B0VX51 from UniProtKB/TrEMBL  Length:660

    Alignment length:145
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599     
           B0VX51_HEV   460 RPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPH 604
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SP2-3rkdB01 B:460-603                                                                                                                           - Pfam domains (1)
           Pfam domains (2) SP2-3rkdB02 B:460-603                                                                                                                           - Pfam domains (2)
         Sec.struct. author ....ee....eeeeeeeeeeee..........eeee..eeeee.....eee.hhhhhhh.ee..ee..eeee..eeeeeee.....eeee..................eeeee......eeee..........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd B 460 RPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQHSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPP 604
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599     


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with CAPSD_HEVPA | P33426 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:145
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599     
          CAPSD_HEVPA   460 RPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQYSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPH 604
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SP2-3rkdB01 B:460-603                                                                                                                           - Pfam domains (1)
           Pfam domains (2) SP2-3rkdB02 B:460-603                                                                                                                           - Pfam domains (2)
         Sec.struct. author ....ee....eeeeeeeeeeee..........eeee..eeeee.....eee.hhhhhhh.ee..ee..eeee..eeeeeee.....eeee..................eeeee......eeee..........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd B 460 RPFSVLRANDVLWLSLTAAEYDQSTYGSSTGPVYVSDSVTLVNVATGAQAVARSLDWTKVTLDGRPLSTIQQHSKTFFVLPLRGKLSFWEAGTTKAGYPYNYNTTASDQLLVENAAGHRVAISTYTTSLGAGPVSISAVAVLAPP 604
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599     


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3rkdc1 C:1-107 automated matches                                                                          d3rkdc2 C:108-213 automated matches                                                                        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.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd C   1 DIQMTQSPASLSVSVGETVTITCRASEIIYSNLAWYQQKQGKSPQLLVYSATNLAEGVPSRFSGSGSGTQYSLKINSLQSEDFGSYYCQHFWGNPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeeee...eeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhhhhh.eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd D   1 QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDVKRYSPALKSRLTISKDTSSSQLFLKIASVDTADTATYYCARIKSVITTGDYALDYWGQGTSVAVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       146       156       166       176       186       196       206       216        
                                                                                                                                                                   138|                                                                               
                                                                                                                                                                    145                                                                               


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee.......eeeee.....eeeeee...hhhhheeeeeeeeeee...eeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhhhhh.eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd H   1 QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDVKRYSPALKSRLTISKDTSSSQLFLKIASVDTADTATYYCARIKSVITTGDYALDYWGQGTSVAVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       146       156       166       176       186       196       206       216        
                                                                                                                                                                   138|                                                                               
                                                                                                                                                                    145                                                                               


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3rkdl1 L:1-107 automated matches                                                                          d3rkdl2 L:108-213 automated matches                                                                        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.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkd L   1 DIQMTQSPASLSVSVGETVTITCRASEIIYSNLAWYQQKQGKSPQLLVYSATNLAEGVPSRFSGSGSGTQYSLKINSLQSEDFGSYYCQHFWGNPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RKD)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Family: SP2 (4)
(-)
Hepatitis E virus (HEV) (3)
1aSP2-3rkdB01B:460-603
1bSP2-3rkdB02B:460-603

(-) Gene Ontology  (7, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CAPSD_HEVPA | P33426)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0039615    T=1 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=1 symmetry. The T=1 capsid is composed of 12 pentameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044228    host cell surface    The external part of the host cell wall and/or host plasma membrane.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain A,B   (B0VX51_HEV | B0VX51)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044228    host cell surface    The external part of the host cell wall and/or host plasma membrane.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  3rkd
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  CAPSD_HEVPA | P33426
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_HEVPA | P33426: 3ggq

(-) Related Entries Specified in the PDB File

3rkc