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(-) Description

Title :  STRUCTURAL BASIS FOR BROAD DETECTION OF GENOGROUP II NOROVIRUSES BY A MONOCLONAL ANTIBODY THAT BINDS TO A SITE OCCLUDED IN THE VIRAL PARTICLE
 
Authors :  G. S. Hansman, J. S. Mclellan, P. D. Kwong
Date :  20 Dec 11  (Deposition) - 08 Feb 12  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,E,F,G,H
Keywords :  Virus, Protein-Fab Complex, Broadly-Reactive Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Hansman, D. W. Taylor, J. S. Mclellan, T. J. Smith, I. Georgiev, J. R. Tame, S. Y. Park, M. Yamazaki, F. Gondaira, M. Miki, K. Katayama, K. Murata, P. D. Kwong
Structural Basis For Broad Detection Of Genogroup Ii Noroviruses By A Monoclonal Antibody That Binds To A Site Occluded In The Viral Particle.
J. Virol. V. 86 3635 2012
PubMed-ID: 22278249  |  Reference-DOI: 10.1128/JVI.06868-11

(-) Compounds

Molecule 1 - 5B18 HEAVY CHAIN
    Chains: F, E
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 5B18 KAPPA CHAIN
    Chains: G, H
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - CAPSID
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: MODIFIED PMAL-C2X
    Fragment: P DOMAIN RESIDUES 224-538
    Organism Scientific: HUMAN CALICIVIRUS
    Organism Taxid: 150080
    Strain: 026VIENTNAM

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABEFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3V7A)

(-) Sites  (0, 0)

(no "Site" information available for 3V7A)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1E:22 -E:96
2E:147 -E:202
3F:22 -F:96
4F:147 -F:202
5G:23 -G:88
6G:135 -G:195
7H:23 -H:88
8H:135 -H:195

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Phe F:153 -Pro F:154
2Glu F:155 -Pro F:156
3Trp F:195 -Pro F:196
4Ser G:7 -Pro G:8
5Pro G:95 -Pro G:96
6Tyr G:141 -Pro G:142
7Phe E:153 -Pro E:154
8Glu E:155 -Pro E:156
9Trp E:195 -Pro E:196
10Ser H:7 -Pro H:8
11Pro H:95 -Pro H:96
12Tyr H:141 -Pro H:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V7A)

(-) Exons   (0, 0)

(no "Exon" information available for 3V7A)

(-) 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:315
 aligned with Q5F4T5_9CALI | Q5F4T5 from UniProtKB/TrEMBL  Length:548

    Alignment length:315
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533     
         Q5F4T5_9CALI   224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee..............ee...ee......hhhhh..eeeeeeeee......eeeeeeee........................eeeeeeeee............eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v7a A 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533     


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q5F4T5_9CALI | Q5F4T5 from UniProtKB/TrEMBL  Length:548

    Alignment length:314
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    
         Q5F4T5_9CALI   225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee..............ee...ee......hhhhh..eeeeeeeee......eeeeeeee........................eeeeeeeee....-----...eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v7a B 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNT-----NLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294       304       314       324       334       344|     |354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    
                                                                                                                                                  345   351                                                                                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee..hhhh.eeeee.hhh.eeeeee...hhhhheeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh....eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v7a E   1 QVQLQQSGAELVRPGTSVKVSCKASGYAFTNYLIEWVKQRPGQGLEWIGVINPRSGDTNSNEKFKGKAILTADKSSSTAYMQLSSLTSDDSAVYFCARSGTTAYFAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain F from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee..hhhh.eeeee.hhh.eeeeee...hhhhheeeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee........eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v7a F   1 QVQLQQSGAELVRPGTSVKVSCKASGYAFTNYLIEWVKQRPGQGLEWIGVINPRSGDTNSNEKFKGKAILTADKSSSTAYMQLSSLTSDDSAVYFCARSGTTAYFAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain G from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee......eeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee...ee...ee............eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v7a G   1 DIQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNVKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGSPPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee......eeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee............eeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee...ee...ee............eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v7a H   1 DIQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNVKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGSPPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 215
                                    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)

(no "SCOP Domain" information available for 3V7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V7A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3V7A)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3v7a)
 
  Sites
(no "Sites" information available for 3v7a)
 
  Cis Peptide Bonds
    Glu E:155 - Pro E:156   [ RasMol ]  
    Glu F:155 - Pro F:156   [ RasMol ]  
    Phe E:153 - Pro E:154   [ RasMol ]  
    Phe F:153 - Pro F:154   [ RasMol ]  
    Pro G:95 - Pro G:96   [ RasMol ]  
    Pro H:95 - Pro H:96   [ RasMol ]  
    Ser G:7 - Pro G:8   [ RasMol ]  
    Ser H:7 - Pro H:8   [ RasMol ]  
    Trp E:195 - Pro E:196   [ RasMol ]  
    Trp F:195 - Pro F:196   [ RasMol ]  
    Tyr G:141 - Pro G:142   [ RasMol ]  
    Tyr H:141 - Pro H:142   [ RasMol ]  
 

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  3v7a
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 Related Entries

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

UniProtKB/TrEMBL
        Q5F4T5_9CALI | Q5F4T5: 3onu 3ony 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3ry8 4x7e 4x7f 4z4r 4z4s 4z4t 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

3onu