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(-) Description

Title :  POLIOVIRUS COMPLEXED WITH SOLUBLE, DEGLYCOSYLATED POLIOVIRUS RECEPTOR (PVR) AT 4 DEGREES C
 
Authors :  M. Strauss, D. J. Filman, D. M. Belnap, N. Cheng, R. T. Noel, J. M. Hogle
Date :  15 Jan 15  (Deposition) - 11 Feb 15  (Release) - 01 Apr 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  9.00
Chains :  Asym. Unit :  1,2,3,4,7,8,9
Biol. Unit 1:  1,2,3,4,7,8,9  (60x)
Keywords :  Deglycosylated Receptor, Picornavirus, Pvr, Cd155, Enterovirus, Cell Entry, Virus-Cell Adhesion Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Strauss, D. J. Filman, D. M. Belnap, N. Cheng, R. T. Noel, J. M. Hogle
Nectin-Like Interactions Between Poliovirus And Its Recepto Trigger Conformational Changes Associated With Cell Entry.
J. Virol. V. 89 4143 2015
PubMed-ID: 25631086  |  Reference-DOI: 10.1128/JVI.03101-14

(-) Compounds

Molecule 1 - PROTEIN VP1
    Chains: 1
    Fragment: UNP RESIDUES 580-881
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Synonym: P1D, VIRION PROTEIN 1
 
Molecule 2 - PROTEIN VP2
    Chains: 2
    Fragment: UNP RESIDUES 70-341
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Synonym: P1B, VIRION PROTEIN 2
 
Molecule 3 - PROTEIN VP3
    Chains: 3
    Fragment: UNP RESIDUES 342-579
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Synonym: P1C, VIRION PROTEIN 3
 
Molecule 4 - PROTEIN VP4
    Chains: 4
    Fragment: UNP RESIDUES 2-69
    Organism Scientific: HUMAN POLIOVIRUS 1 MAHONEY
    Organism Taxid: 12081
    Synonym: P1A, VIRION PROTEIN 4
 
Molecule 5 - POLIOVIRUS RECEPTOR
    Chains: 7
    Fragment: SEE REMARK 999
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-LIKE PROTEIN 5, NECL-5, PVR, CD155
 
Molecule 6 - POLIOVIRUS RECEPTOR
    Chains: 8
    Fragment: SEE REMARK 999
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-LIKE PROTEIN 5, NECL-5, PVR, CD155
 
Molecule 7 - POLIOVIRUS RECEPTOR
    Chains: 9
    Fragment: SEE REMARK 999
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-LIKE PROTEIN 5, NECL-5, PVR, CD155

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : 1234789
Biological Unit 1 (60x): 1234789

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric Unit (6, 22)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4MYR1Mod. Amino AcidMYRISTIC ACID
5NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PLM1Ligand/IonPALMITIC ACID
Biological Unit 1 (6, 1320)
No.NameCountTypeFull Name
1BMA240Ligand/IonBETA-D-MANNOSE
2FUC120Ligand/IonALPHA-L-FUCOSE
3MAN60Ligand/IonALPHA-D-MANNOSE
4MYR60Mod. Amino AcidMYRISTIC ACID
5NAG780Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PLM60Ligand/IonPALMITIC ACID

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR 1:112 , MET 1:132 , LEU 1:134 , TYR 1:159 , TYR 1:205 , PHE 1:237BINDING SITE FOR RESIDUE PLM 1 901
02AC2SOFTWARETYR 7:50 , VAL 7:95 , ALA 7:96 , ASN 7:105 , NAG 7:402BINDING SITE FOR RESIDUE NAG 7 401
03AC3SOFTWARENAG 7:401 , BMA 7:403BINDING SITE FOR RESIDUE NAG 7 402
04AC4SOFTWARENAG 7:402BINDING SITE FOR RESIDUE BMA 7 403
05AC5SOFTWAREGLY 7:119 , ASN 7:120 , TRP 7:138 , NAG 7:405 , FUC 7:406BINDING SITE FOR RESIDUE NAG 7 404
06AC6SOFTWARETRP 7:138 , NAG 7:404 , BMA 7:407BINDING SITE FOR RESIDUE NAG 7 405
07AC7SOFTWAREASN 7:120 , NAG 7:404BINDING SITE FOR RESIDUE FUC 7 406
08AC8SOFTWARENAG 7:405 , MAN 7:408BINDING SITE FOR RESIDUE BMA 7 407
09AC9SOFTWAREBMA 7:407BINDING SITE FOR RESIDUE MAN 7 408
10BC1SOFTWAREASN 8:188 , NAG 8:302BINDING SITE FOR RESIDUE NAG 8 301
11BC2SOFTWARENAG 8:301BINDING SITE FOR RESIDUE NAG 8 302
12BC3SOFTWAREASN 8:218 , NAG 8:304 , NAG 8:305BINDING SITE FOR RESIDUE NAG 8 303
13BC4SOFTWARENAG 8:303BINDING SITE FOR RESIDUE NAG 8 304
14BC5SOFTWAREGLY 8:216 , ASN 8:218 , ASN 8:237 , NAG 8:303 , NAG 8:306BINDING SITE FOR RESIDUE NAG 8 305
15BC6SOFTWARENAG 8:305 , BMA 8:307BINDING SITE FOR RESIDUE NAG 8 306
16BC7SOFTWARENAG 8:306BINDING SITE FOR RESIDUE BMA 8 307
17BC8SOFTWAREPRO 9:305 , ASN 9:307 , FUC 9:402 , NAG 9:403BINDING SITE FOR RESIDUE NAG 9 401
18BC9SOFTWARENAG 9:401 , NAG 9:403BINDING SITE FOR RESIDUE FUC 9 402
19CC1SOFTWARENAG 9:401 , FUC 9:402 , BMA 9:404BINDING SITE FOR RESIDUE NAG 9 403
20CC2SOFTWARENAG 9:403BINDING SITE FOR RESIDUE BMA 9 404
21CC3SOFTWAREASN 9:313 , THR 9:315 , GLN 9:322BINDING SITE FOR RESIDUE NAG 9 405

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
17:49 -7:123
28:166 -8:221
39:266 -9:312

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu 2:82 -Pro 2:83
2Pro 7:38 -Gly 7:39
3Phe 7:128 -Pro 7:129
4Arg 8:172 -Pro 8:173
5Asn 9:271 -Pro 9:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J9F)

(-) Exons   (0, 0)

(no "Exon" information available for 3J9F)

(-) 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.....hhhhh...........hhhhhhhhhhh..eeeeeeeeee...........eeee......hhhhhhhh.eeeeeeeeeeeeeeeeee...........eeeeeee...........hhhhhh....eeeee.....eeeee........ee.........................hhhhh..eeeeee........eeeeeeeeeeeeeeeeeee............................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j9f 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........hhhhh...ee...eeee.....eeeeehhhhh.hhhhhhhhhheeeeeeeeeeeee......eeeeeeeeeee...............hhhhhhhhhhhee....................hhhhh....hhhhhhhh.eeeee.....eeeeee................eeeeeeeeeeeee......eeeeeeeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j9f 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..ee...........hhhhhheeee.........eeee...........hhhhhhhh.eeeee..eeeeeee........eeeeeee........hhhhhh..eeeeee.....eeeeee........ee..........eeeeee............eeeeeeeeee....eeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j9f 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
                 3j9f 4   1 xGAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLN  69
                            |       10        20        30        40        50        60         
                            1-MYR                                                                


Chain 7 from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...ee.......eee..eee..........eeeeee.......eeee...eeee.....eee.............eee...hhhhheeeeeeee.....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3j9f 7  28 DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVLA 143
                                    37        47        57        67        77        87        97       107       117       127       137      


Chain 8 from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeeee....eeeeee....eeeeeeee......eeeeeeeee..hhhhh..eeeeeee.......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3j9f 8 142 LAKPQNTAEVQKVQLTGEPVPMARCVSTGGRPPAQITWHSDLGGMPNTSQVPGFLSGTVTVTSLWILVPSSQVDGKNVTCKVEHESFEKPQLLTVNLTVYYP 243
                                   151       161       171       181       191       201       211       221       231       241  


Chain 9 from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....ee.....eeeeeeee......eeeeee........eeee..eeee.......eeeeeeeee....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3j9f 9 242 YPPEVSISGYDNNWYLGQNEATLTCDARSNPEPTGYNWSTTMGPLPPFAVAQGAQLLIRPVDKPINTTLICNVTNALGARQAELTVQVKEGP 333
                                   251       261       271       281       291       301       311       321       331
   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 3J9F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J9F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J9F)

(-) Gene Ontology  (74, 77)

Asymmetric Unit(hide GO term definitions)

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  3j9f
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  POLG_POL1M | P03300
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  PVR_HUMAN | P15151
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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 3jbc 3jbd 3jbe 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
        PVR_HUMAN | P15151: 1dgi 1nn8 3epc 3epd 3epf 3j8f 3udw 3uro 4fqp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3J9F)