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(-) Description

Title :  EXPANDED POLIOVIRUS IN COMPLEX WITH VHH 12B
 
Authors :  M. Strauss, L. Schotte, D. J. Filman, J. M. Hogle
Date :  12 Jul 16  (Deposition) - 02 Nov 16  (Release) - 08 Feb 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.30
Chains :  Asym. Unit :  1,2,3,7
Biol. Unit 1:  1,2,3,7  (60x)
Keywords :  Poliovirus, Vhh, Nanobody, 80S, Expanded, Single Domain Antibody, Virus-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Strauss, L. Schotte, K. S. Karunatilaka, D. J. Filman, J. M. Hogle
Cryo-Electron Microscopy Structures Of Expanded Poliovirus With Vhhs Sample The Conformational Repertoire Of The Expanded State.
J. Virol. V. 91 2017
PubMed-ID: 27852863  |  Reference-DOI: 10.1128/JVI.01443-16

(-) Compounds

Molecule 1 - VP1
    Chains: 1
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 636-858
    Organism Scientific: POLIOVIRUS TYPE 1 (STRAIN MAHONEY)
    Organism Taxid: 12081
    Strain: MAHONEY
 
Molecule 2 - VP2
    Chains: 2
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 70-338
    Organism Scientific: POLIOVIRUS TYPE 1 (STRAIN MAHONEY)
    Organism Taxid: 12081
    Strain: MAHONEY
 
Molecule 3 - GENOME POLYPROTEIN
    Chains: 3
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 342-572
    Organism Scientific: POLIOVIRUS TYPE 1
    Organism Taxid: 12081
    Strain: MAHONEY
 
Molecule 4 - VHH 12B
    Chains: 7
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Organism Common: ARABIAN CAMEL
    Organism Scientific: CAMELUS DROMEDARIUS
    Organism Taxid: 9838

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : 1237
Biological Unit 1 (60x): 1237

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5KTZ)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
17:22 -7:96

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu 2:82 -Pro 2:83
2Asn 2:261 -Gly 2:262
3Phe 7:100 -Gly 7:101
4Gly 7:101 -Leu 7:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KTZ)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhh..eeeeeee..............eeee.hhhhhhhhhhhhh.eeeeeeeeeeeeeeeeee...........eeeeeee...........hhhhh......eeee.....eeeee........ee..............eeeeee........eeeeeeeeeeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ktz 1  57 PSDTVQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAY 279
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      |234       244       254       264       274     
                                                                                                                                                                                      213|                                               
                                                                                                                                                                                       232                                               


Chain 2 from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............................ee.hhh.........hhhhh...ee...eee......ee...hhhhhhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeee.................hhhhhh.............hhhhh....hhhhhhhh.eeeee.....eeeeee..................eeeeeeeeeee.......eeeeeee.eeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ktz 2   1 SPNIEACGYSDRVLQLTLGNSTITTQEAANSVVAYGRWPEYLRPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITLTIAPMCCEFNGLRNITLP 269
                                    10        20        30        40  ||    59        69        79        89        99       109       119       129       139       149       159|      183       193       203       213       223       233       243       253       263      
                                                                     43|                                                                                                       159|                                                                                               
                                                                      53                                                                                                        174                                                                                               


Chain 3 from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................ee..hhhhhh..ee...........hhhhhheee..........eeee.hhhhh.....hhhhhhhh...ee...eeeeeeee.....eeeeeeeee........hhhhhhhh.eeeee.....eeeeee........ee..........eeeee....ee........eeeeeeeee.....ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ktz 3   1 GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHI 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 


Chain 7 from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeeeee........eeeeee.......eeeeeee...............eeeeee....eeeeee...........eeeee.........eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ktz 7   1 QVQLQESGGGSVQAGGSLTLSCAASGYAVSRYSMGWFRQAPGKENEGVAAIDSSGVGTTYADSVKGRFTISRDNAKDTVYLRMNSLKPEDTAIYYCASGFGLSLSRYTYAYWGQGTQVTVSSH 123
                                    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 5KTZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

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  Cis Peptide Bonds
    Asn 2:261 - Gly 2:262   [ RasMol ]  
    Gly 7:101 - Leu 7:102   [ RasMol ]  
    Leu 2:82 - Pro 2:83   [ RasMol ]  
    Phe 7:100 - Gly 7:101   [ RasMol ]  
 
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  5ktz
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  POLG_POL1M | P03300
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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 3jbe 3jbf 3jbg 3ol7 4dcd 4k4s 4k4t 4k4u 4k4v 4k4w 4nlo 4nlp 4nlq 4nlr 4nls 4nlt 4nlu 4nlv 4nlw 4nlx 4nly 4r0e 5ku0 5ku2 5kwl

(-) Related Entries Specified in the PDB File

5ku0 5ku2