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(-) Description

Title :  CRYSTAL STRUCTURE OF NOROVIRUS GII.10 P DOMAIN IN COMPLEX WITH NANO-25
 
Authors :  A. D. Koromyslova, G. S. Hansman
Date :  09 Dec 14  (Deposition) - 31 Dec 14  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nanobody, Vhh Domain, Norovirus, Protruding Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Koromyslova, G. S. Hansman
Nanobody Binding To A Conserved Epitope Promotes Norovirus Particle Disassembly.
J. Virol. V. 89 2718 2015
PubMed-ID: 25520510  |  Reference-DOI: 10.1128/JVI.03176-14

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMBP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VHH, UNP RESIDUES 224-538
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
 
Molecule 2 - NANO-25 NANOBODY
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: WK6
    Expression System Plasmid: PHEN6C
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric/Biological Unit (4, 27)
No.NameCountTypeFull Name
1EDO23Ligand/Ion1,2-ETHANEDIOL
2IMD2Ligand/IonIMIDAZOLE
3NA1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:269 , ARG A:501binding site for residue NA A 601
02AC2SOFTWAREASN A:309 , LEU A:310 , ASN A:311 , HOH A:736 , HOH A:758 , HOH A:799binding site for residue EDO A 602
03AC3SOFTWARELEU A:279 , THR A:281 , GLY A:282 , HOH A:741 , HOH A:748binding site for residue EDO A 603
04AC4SOFTWAREPHE A:408 , GLN A:410 , PRO A:455 , ALA A:456 , HOH A:774binding site for residue EDO A 604
05AC5SOFTWAREARG A:341 , HOH A:742 , PHE B:445 , PRO B:447binding site for residue EDO A 605
06AC6SOFTWARELEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:325 , HOH A:870binding site for residue EDO A 606
07AC7SOFTWAREGLN A:277 , LEU A:278 , GLU B:236 , HOH B:765binding site for residue EDO A 607
08AC8SOFTWAREVAL A:361 , SER A:379 , THR A:380binding site for residue EDO A 608
09AC9SOFTWARETHR A:233 , GLY A:235 , EDO B:605binding site for residue EDO A 609
10AD1SOFTWAREASP A:247 , EDO B:604binding site for residue EDO A 610
11AD2SOFTWARETYR A:470 , GLN A:471 , HIS C:114binding site for residue EDO A 611
12AD3SOFTWAREGLU A:236 , HOH A:812 , GLN B:277 , LEU B:278binding site for residue EDO A 612
13AD4SOFTWAREASP A:316 , THR A:318 , LEU A:494 , PHE A:495 , VAL A:515 , VAL A:516 , HOH A:703 , HOH A:704binding site for residue EDO A 613
14AD5SOFTWAREARG A:287 , ASN A:311 , HOH A:782 , PRO B:245 , ILE B:246 , ASP B:247 , HOH B:775binding site for residue EDO A 614
15AD6SOFTWAREHIS A:358 , GLU A:359 , GLU A:382 , HOH A:784 , HOH A:874 , GLU B:359 , LYS B:449binding site for residue PO4 A 615
16AD7SOFTWAREPHE B:408 , GLN B:410 , PRO B:455 , ALA B:456 , HOH B:741 , HOH B:791 , HOH B:889binding site for residue EDO B 601
17AD8SOFTWARELEU B:234 , VAL B:248 , LEU B:249 , VAL B:515 , ALA B:517 , THR B:519 , HOH B:856binding site for residue EDO B 602
18AD9SOFTWARELEU B:272 , GLN B:273 , GLY B:274 , THR B:276 , LEU B:325 , HOH B:837binding site for residue EDO B 603
19AE1SOFTWAREPHE A:445 , PRO A:447 , EDO A:610 , ARG B:341 , HOH B:772binding site for residue EDO B 604
20AE2SOFTWAREEDO A:609 , ASN B:309 , LEU B:310 , ASN B:311 , HOH B:739 , HOH B:807 , HOH B:810binding site for residue EDO B 605
21AE3SOFTWARETYR B:470 , GLN B:471 , SER B:473 , HOH B:805binding site for residue EDO B 606
22AE4SOFTWARETHR B:318 , GLU B:319 , ASP B:320 , LYS B:372 , ASN B:425binding site for residue EDO B 607
23AE5SOFTWAREPRO A:245 , THR B:281 , GLY B:282 , LEU B:310 , LYS B:393 , HOH B:754 , HOH B:762 , HOH B:879binding site for residue EDO B 608
24AE6SOFTWAREPRO A:243 , PRO A:280 , HOH A:806 , PRO B:243 , PRO B:280 , THR B:281 , HOH B:756binding site for residue IMD B 609
25AE7SOFTWAREPHE A:434 , PRO A:435 , GLU C:46 , LEU C:47binding site for residue EDO C 201
26AE8SOFTWAREASP A:479 , GLN A:531 , THR C:52 , SER C:56 , THR C:57 , HOH C:302binding site for residue IMD C 202
27AE9SOFTWAREARG D:38 , GLU D:46 , ALA D:60 , SER D:62 , HOH D:328binding site for residue EDO D 201

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1C:22 -C:95
2D:22 -D:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X7F)

(-) Exons   (0, 0)

(no "Exon" information available for 4X7F)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeee......eeeeeee.........................eeeeeeeee.......eeeeeeeeee......hhhh.eeeeee..........eeeeeeeeeee.hhhhh............................eeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x7f A 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294       304       314       324       334       344||     359       369       379       389       399       409       421       431       441       451       461       471       481       491       501       511       521       531       
                                                                                                                                                  345|                                                                418|                                                                                                                     
                                                                                                                                                   351                                                                 421                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeeeee...eeeeee.........................eeeeeeeee....eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x7f B 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVHRTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   233       243       253       263       273       283       293||||   307       317       327       337     ||355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535   
                                                                                                294|||                                       343|                                                                                                                                                                                          
                                                                                                 298||                                        352                                                                                                                                                                                          
                                                                                                  299|                                                                                                                                                                                                                                     
                                                                                                   301                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eee.....eeeeeee..hhhhh.eeeeeee......eeeeeee....eee.......eeeee.....eeeeee...hhhhheeeeee..........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4x7f C   1 DVQLVESGGGLVQPGGSLRLSCAASESILSFNHMAWYRQGPGEQRELVAVITREGSTDYADSVKGRFTISRDNAKNMVYLLMSNLRPEDTAVYYCNRGISNPWGQGTQVTVSSH 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain D from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee..hhhhh.eeeeeee......eeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4x7f D   1 DVQLVESGGGLVQPGGSLRLSCAASESILSFNHMAWYRQGPGEQRELVAVITREGSTDYADSVKGRFTISRDNAKNMVYLLMSNLRPEDTAVYYCNRGISNPWGQGTQVTVS 112
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4X7F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X7F)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4X7F)

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        Q5F4T5_9CALI | Q5F4T5: 3onu 3ony 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3ry8 3v7a 4x7e 4z4r 4z4s 4z4t 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

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