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(-) Description

Title :  CRYOEM STRUCTURE OF RHINOVIRUS B14 IN COMPLEX WITH C5 FAB (33 DEGREES CELSIUS, MOLAR RATIO 1:3, EMPTY PARTICLE)
 
Authors :  Y. Liu, Y. Dong, M. G. Rossmann
Date :  08 Jun 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.01
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (60x)
Keywords :  Virus, Antibody, Virus Like Particle-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Dong, Y. Liu, W. Jiang, T. J. Smith, Z. Xu, M. G. Rossmann
Antibody Induced Uncoating Of Human Rhinovirus B14
Proc. Natl. Acad. Sci. Usa 2017
PubMed: search  |  Reference-DOI: 10.1073/PNAS.1707369114

(-) Compounds

Molecule 1 - C5 ANTIBODY VARIABLE HEAVY DOMAIN
    Chains: D
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - C5 ANTIBODY VARIABLE LIGHT DOMAIN
    Chains: E
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - VIRAL PROTEIN 1
    Chains: A
    Fragment: UNP RESIDUES 568-856
    Organism Common: HRV-14, HUMAN RHINOVIRUS B14
    Organism Scientific: HUMAN RHINOVIRUS 14
    Organism Taxid: 12131
 
Molecule 4 - VIRAL PROTEIN 3
    Chains: B
    Fragment: UNP RESIDUES 332-567
    Organism Common: HRV-14, HUMAN RHINOVIRUS B14
    Organism Scientific: HUMAN RHINOVIRUS 14
    Organism Taxid: 12131
 
Molecule 5 - VIRAL PROTEIN 2
    Chains: C
    Fragment: UNP RESIDUES 70-331
    Organism Common: HRV-14, HUMAN RHINOVIRUS B14
    Organism Scientific: HUMAN RHINOVIRUS 14
    Organism Taxid: 12131

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (60x): ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5W3O)

(-) Sites  (0, 0)

(no "Site" information available for 5W3O)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1D:22 -D:95
2E:23 -E:88

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser E:7 -Pro E:8
2Thr E:94 -Pro E:95
3Leu C:82 -Pro C:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5W3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5W3O)

(-) Exons   (0, 0)

(no "Exon" information available for 5W3O)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...eeeeeeeeee..............eeeee.hhhhhhhhhhhhh.eeeeeee..eeeeee.............eeeeeee............hhhhh....eeeee...eeee..........ee.................hhhhh..eeeeee........eeeeeeeee..eeeeeeee.................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w3o A  61 NGSETDVECFLGRAACVHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFTYVRFDSEYTILATASQPDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKVGDTSRFSVPYVGLASAYNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVKIRVYHRAKHVEAWIPRAPRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY 289
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................ee..........ee..........hhhh.eeeee......eeeeee....hhhhh.hhhhhhhh.eee....eeeeeee........eeeeeee........hhhhhhhheeeeee.....eeeeee..........eeeeee............eeeeeeeeee......eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w3o B   3 PTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHTKDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGPALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQT 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       182       192       202       212       222     
                                                                                                                                                                                                  171|                                             
                                                                                                                                                                                                   182                                             


Chain C from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eee.......eee.hhh............ee...eeee.....eeeeehhhhh.hhhhhhhhhhh.eeeeeeeeeee.........eeeeeeee..............hhhhhh.....ee............hhhhh....hhhhhhh..eeeee.....eeeeee........ee......eeeeeee............eeeeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5w3o C  13 VQQITLGNSTITTQEAANAVVCYAEWPEYLDTSVCRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSGCLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSANEVGGPVKDVIYNMNGTLLGNLLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPIAPLTVPTGATPSLPITVTIAPMCTEFSGIRSKSIV 260
                                    22        32        42|       66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256    
                                                        42|                                                                                                                                                                                                           
                                                         57                                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.......eeeeee........eeeeee......eeeeee.....eee........eeeee....eeeee....hhhhheeeee..............eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5w3o D   1 AVQLAESGPALVAPSQALSITCTVAGFSLTAYGVAWVRQPPGAGLEWLGAIWAAGATDYNAALKSRASIAKDNSKSQVFLAMASLATADTAAYYCAREWDAYGDYWGQGTTVTVSA 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain E from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eee.....eeeeee.........eeeeee...........eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5w3o E   1 DIVLTQSPAALSAAAGATVAATCRASGNIHNALAWYQQKAGKSPQLLVYAAAALAAGVPSRFSGSGSGTAYALAINSLAADDFGAYYCQHFWSTPYTFGGGTKLEIK 107
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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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 5W3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5W3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5W3O)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5W3O)

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  Sites
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  Cis Peptide Bonds
    Leu C:82 - Pro C:83   [ RasMol ]  
    Ser E:7 - Pro E:8   [ RasMol ]  
    Thr E:94 - Pro E:95   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HRV14 | P03303: 1d3i 1hri 1hrv 1k5m 1na1 1ncq 1r08 1r09 1rmu 1ruc 1rud 1rue 1ruf 1rug 1ruh 1rui 1ruj 1rvf 1vrh 1xr5 2b0f 2hwb 2hwc 2in2 2r04 2r06 2r07 2rm2 2rmu 2rr1 2rs1 2rs3 2rs5 4pdw 4rhv 5w3e 5w3l 5w3m

(-) Related Entries Specified in the PDB File

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