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(-) Description

Title :  COMPLEX OF POLIOVIRUS WITH VHH PVSS8A
 
Authors :  M. Strauss, L. Schotte, B. Thys, D. J. Filman, J. M. Hogle
Date :  26 Aug 15  (Deposition) - 27 Jan 16  (Release) - 30 Mar 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.20
Chains :  Asym. Unit :  1,2,3,4,7
Biol. Unit 1:  1,2,3,4,7  (60x)
Keywords :  Poliovirus, Nanobodies, Vhh, Neutralizing Antibodies, Virus-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Strauss, L. Schotte, B. Thys, D. J. Filman, J. M. Hogle
Five Of Five Vhhs Neutralizing Poliovirus Bind The Receptor-Binding Site.
J. Virol. V. 90 3496 2016
PubMed-ID: 26764003  |  Reference-DOI: 10.1128/JVI.03017-15

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: 1
    Fragment: UNP RESIDUES 580-881
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Strain: MAHONEY
    Synonym: P1D, VIRION PROTEIN 1
 
Molecule 2 - CAPSID PROTEIN VP2
    Chains: 2
    Fragment: UNP RESIDUES 70-341
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Strain: MAHONEY
    Synonym: P1B, VIRION PROTEIN 2
 
Molecule 3 - CAPSID PROTEIN VP3
    Chains: 3
    Fragment: UNP RESIDUES 342-578
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Strain: MAHONEY
    Synonym: P1C, VIRION PROTEIN 3
 
Molecule 4 - CAPSID PROTEIN VP4
    Chains: 4
    Fragment: UNP RESIDUES 2-69
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Strain: MAHONEY
    Synonym: P1A, VIRION PROTEIN 4
 
Molecule 5 - NANOBODY VHH PVSS8A
    Chains: 7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: ARABIAN CAMEL
    Organism Scientific: CAMELUS DROMEDARIUS
    Organism Taxid: 9838

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : 12347
Biological Unit 1 (60x): 12347

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MYR1Mod. Amino AcidMYRISTIC ACID
2PLM1Ligand/IonPALMITIC ACID
Biological Unit 1 (2, 120)
No.NameCountTypeFull Name
1MYR60Mod. Amino AcidMYRISTIC ACID
2PLM60Ligand/IonPALMITIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE 1:110 , TYR 1:112 , PHE 1:130 , MET 1:132 , LEU 1:134 , TYR 1:159 , ILE 1:194 , VAL 1:196 , VAL 1:199 , TYR 1:205 , SER 1:206 , HIS 1:207 , ASN 1:235 , PHE 1:237 , LEU 1:240BINDING SITE FOR RESIDUE PLM 1 901

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
17:22 -7:96
27:33 -7:107

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu 2:82 -Pro 2:83
2Ser 7:7 -Gly 7:8
3Ser 7:25 -Gly 7:26
4Glu 7:43 -Gly 7:44
5Gly 7:112 -Tyr 7:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JBE)

(-) 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 1 from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eehhhhh.....hhhhhh.........hhhhhhhhhhhh..eeeeeeeeee...........eeee.hhhhhhhhhhhhhheeeeeeeeeeeeeeeeee...........eeeeeee...........hhhhhh....eeeee.....eeeee........ee..............hhhhhh.....hhhhh..eeeeee........eeeeeeeeeeeeeeeeeee............................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jbe 1  20 AATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDTVQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY 302
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   


Chain 2 from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..eeeee......ee.hhh..................hhhhh...ee...eee......eeee.hhhhhhhhhhhhhhhheeeeeeeeeeeee......eeeeeeeeeee...............hhhhhh.....ee....................hhhhh....hhhhhhhh.eeeee.....eeeeee................eeeeeeeeeeeee.......eeeeeeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jbe 2   6 ACGYSDRVLQLTLGNSTITTQEAANSVVAYGRWPEYLRDSEANPVDQPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITLTIAPMCCEFNGLRNITLPRLQ 272
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       


Chain 3 from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................ee.hhhhhhh..eee..........hhhhhhee...........eeee...........hhhhhhhh...eee..eeeeeee.........eeeeee........hhhhhhhheeee.......eeeeee........ee..........eeeeee..............eeeeeeee....eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jbe 3   1 GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKA 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     


Chain 4 from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeee.....hhhhh..........hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 3jbe 4   1 xGAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLN  69
                            |       10        20        30        40        50        60         
                            1-MYR                                                                


Chain 7 from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..eeee..eeeeeeee...........eeeee......eeeeee......eee.......eeeeee....eeeeeeeee.....eeeeee.......................eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jbe 7   1 QVQLQESGGGSVQAGGSLRLSCAASGYQYSLLCMAWFRQVLGEGREGVAFITTYNGAMRYADTVKGRFTVSQDKDKNTVYLQMNSLKPEDTAIYYCAAGRWRFGDICHEGSGYNYWGQGTQVTVSSH 127
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 3JBE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_POL1M | P03300: 1al2 1ar6 1ar7 1ar8 1ar9 1asj 1dgi 1fpt 1hxs 1l1n 1ng7 1nn8 1po1 1po2 1pov 1ra6 1ra7 1raj 1rdr 1tql 1vbd 1xyr 2bbl 2bbp 2ijd 2ijf 2ily 2ilz 2im0 2im1 2im2 2im3 2plv 3epc 3iyb 3iyc 3j3o 3j3p 3j48 3j8f 3j9f 3jbc 3jbd 3jbf 3jbg 3ol7 4dcd 4k4s 4k4t 4k4u 4k4v 4k4w 4nlo 4nlp 4nlq 4nlr 4nls 4nlt 4nlu 4nlv 4nlw 4nlx 4nly 4r0e 5ktz 5ku0 5ku2 5kwl

(-) Related Entries Specified in the PDB File

3jbc 3jbd 3jbf 3jbg