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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NORWALK VIRUS STRAIN VIETNAM 026 IN COMPLEX WITH HBGA TYPE H2 (DIGLYCAN)
 
Authors :  G. S. Hansman, C. Biertumpfel, L. Chen, I. Georgiev, J. S. Mclellan, K. K P. D. Kwong
Date :  21 Dec 10  (Deposition) - 11 May 11  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, P-Domain, Capsid, Receptor, Histo Blood Group Antigen (Hbga), Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Hansman, C. Biertumpfel, I. Georgiev, J. S. Mclellan, L. Chen, T. Zhou, K. Katayama, P. D. Kwong
Crystal Structures Of Gii. 10 And Gii. 12 Norovirus Protrudin Domains In Complex With Histo-Blood Group Antigens Reveal Details For A Potential Site Of Vulnerability.
J. Virol. V. 85 6687 2011
PubMed-ID: 21525337  |  Reference-DOI: 10.1128/JVI.00246-11

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MBP-HTSHP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP REISDUES 224-538
    Gene: CAPSID PROTEIN
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
    Strain: VIETNAM 026

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
1EDO22Ligand/Ion1,2-ETHANEDIOL
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4IMD4Ligand/IonIMIDAZOLE

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGAL A:2 , ALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , HOH A:1063 , HOH A:1160 , HOH B:190 , GLY B:451 , TYR B:452BINDING SITE FOR RESIDUE FUC A 1
02AC2SOFTWAREFUC A:1 , PHE A:532 , THR A:534 , HOH A:1012 , HOH A:1063 , GLY B:451BINDING SITE FOR RESIDUE GAL A 2
03AC3SOFTWAREHOH A:171 , PRO A:245 , ASP A:247 , PHE A:445 , HOH A:1118 , EDO B:16 , ARG B:287BINDING SITE FOR RESIDUE EDO A 854
04AC4SOFTWAREHOH A:61 , LEU A:279 , THR A:281 , GLY A:282 , ARG A:287 , HOH B:69BINDING SITE FOR RESIDUE EDO A 3
05AC5SOFTWAREHOH A:155 , GLU A:236 , HOH A:863 , LEU B:278 , HOH B:1134BINDING SITE FOR RESIDUE EDO A 4
06AC6SOFTWAREHOH A:42 , HOH A:59 , HOH A:67 , PRO A:245 , ILE A:246 , ASN B:311BINDING SITE FOR RESIDUE EDO A 6
07AC7SOFTWAREHOH A:43 , HOH A:153 , PHE A:408 , GLN A:410 , PRO A:455 , ALA A:456 , HOH A:1134BINDING SITE FOR RESIDUE EDO A 7
08AC8SOFTWAREHIS A:302 , ILE A:362 , ALA A:363 , GLN A:377 , PHE A:378 , SER A:379BINDING SITE FOR RESIDUE EDO A 8
09AC9SOFTWAREARG A:287 , ARG A:341 , LYS A:393 , HOH A:1094 , HOH A:1172 , PRO B:447BINDING SITE FOR RESIDUE EDO A 10
10BC1SOFTWAREHOH A:33 , HOH A:48 , HOH A:140 , ASN A:309 , LEU A:310 , ASN A:311 , LEU A:325BINDING SITE FOR RESIDUE EDO A 12
11BC2SOFTWAREGLN A:277 , LEU A:278 , HOH A:1099 , HOH B:91 , GLU B:236 , HOH B:1014BINDING SITE FOR RESIDUE EDO A 13
12BC3SOFTWAREHOH A:30 , HOH A:113 , HOH A:126 , PRO A:243 , PRO A:280 , THR A:281 , HOH A:862 , PRO B:243 , PRO B:280 , THR B:281BINDING SITE FOR RESIDUE EDO A 17
13BC4SOFTWARETYR A:365 , LEU A:413 , SER A:415 , HOH A:1008 , HOH A:1170BINDING SITE FOR RESIDUE EDO A 19
14BC5SOFTWAREARG A:299 , GLY A:300 , SER A:379 , THR A:380 , TRP A:381 , HOH A:1068 , HOH A:1112BINDING SITE FOR RESIDUE EDO A 21
15BC6SOFTWAREHOH A:40 , HIS A:358 , GLU A:359 , TRP A:381 , HOH A:987 , HOH A:1038 , IMD B:23 , GLU B:359 , LYS B:449BINDING SITE FOR RESIDUE EDO A 22
16BC7SOFTWAREGLU A:359 , TRP A:381 , LYS A:449 , HOH A:1014 , HIS B:358BINDING SITE FOR RESIDUE IMD A 24
17BC8SOFTWARELEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:325 , HOH A:1099BINDING SITE FOR RESIDUE IMD A 25
18BC9SOFTWAREHOH A:67 , HOH B:27 , LEU B:279 , THR B:281 , GLY B:282 , ARG B:287BINDING SITE FOR RESIDUE EDO B 1
19CC1SOFTWAREHOH B:36 , HOH B:158 , ASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:857BINDING SITE FOR RESIDUE EDO B 5
20CC2SOFTWAREARG B:299 , SER B:379 , THR B:380 , TRP B:381 , HOH B:1080BINDING SITE FOR RESIDUE EDO B 9
21CC3SOFTWAREHOH B:49 , HOH B:137 , PHE B:408 , GLN B:410 , PRO B:455 , ALA B:456 , HOH B:1073BINDING SITE FOR RESIDUE EDO B 11
22CC4SOFTWAREASN A:311 , HOH B:69 , HOH B:86 , HOH B:107 , PRO B:245 , ILE B:246 , HOH B:1048BINDING SITE FOR RESIDUE EDO B 14
23CC5SOFTWAREPRO B:317 , THR B:318 , GLU B:319 , ASP B:320 , LYS B:372 , ASN B:425BINDING SITE FOR RESIDUE EDO B 15
24CC6SOFTWAREHOH A:128 , PHE A:445 , PRO A:447 , EDO A:854 , HOH B:3 , ARG B:287 , ARG B:341 , HOH B:893BINDING SITE FOR RESIDUE EDO B 16
25CC7SOFTWAREPRO B:230 , LEU B:232 , LEU B:237 , TRP B:465 , PHE B:523 , HOH B:927BINDING SITE FOR RESIDUE EDO B 18
26CC8SOFTWAREVAL B:402 , ASP B:403 , SER B:406 , HIS B:407 , PHE B:408BINDING SITE FOR RESIDUE EDO B 20
27CC9SOFTWAREEDO A:22 , HIS A:358 , GLU B:359 , TRP B:381 , LYS B:449BINDING SITE FOR RESIDUE IMD B 23
28DC1SOFTWARELEU B:272 , GLN B:273 , GLY B:274 , THR B:276 , LEU B:325BINDING SITE FOR RESIDUE IMD B 26

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q39)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q39)

(-) 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...........................hhhhh..eeeeeeeee......eeeeeee.........................eeeeeeeee....hhhhh...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
                 3q39 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:307
 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 (1) Calici_coat-3q39B01 B:224-291                                       ---------------Calici_coat_C-3q39B03 B:307-538                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) Calici_coat-3q39B02 B:224-291                                       ---------------Calici_coat_C-3q39B04 B:307-538                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeeeeeee...eeeeeeee.........................eeeeeeeee..--------..eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q39 B 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNT--------LPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 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     
                                                                                                                                                 343      352
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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 3Q39)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q39)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Calici_coat_C] (19)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3Q39)

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  3q39
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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 3q3a 3q6q 3q6r 3ry8 3v7a 4x7e 4x7f 4z4r 4z4s 4z4t 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

3onu 3ony 3pa1 3pa2 3q38 3q3a 3q6q 3q6r 3r6j 3r6k