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(-) Description

Title :  STRUCTURE OF HUMAN ADENOVIRUS SEROTYPE 37 FIBRE HEAD IN COMPLEX WITH A SIALIC ACID DERIVATIVE, O-METHYL 5-N-METHOXYCARBONYL -3,5-DIDEOXY-D-GLYCERO-A-D-GALACTO-2-NONULOPYRANOSYLONIC ACID
 
Authors :  S. Johansson, E. Nilsson, W. Qian, D. Guilligay, T. Crepin, S. Cusack, N. Arnberg, M. Elofsson
Date :  27 Apr 09  (Deposition) - 24 Nov 09  (Release) - 24 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Sialic Acid, Viral Protein, Conjunctivitis, Daf, Ad37, Cd46, Receptor, Neuraminic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Johansson, E. Nilsson, W. Qian, D. Guilligay, T. Crepin, S. Cusack, N. Arnberg, M. Elofsson
Design, Synthesis, And Evaluation Of N-Acyl Modified Sialic Acids As Inhibitors Of Adenoviruses Causing Epidemic Keratoconjunctivitis.
J. Med. Chem. V. 52 3666 2009
PubMed-ID: 19456100  |  Reference-DOI: 10.1021/JM801609S

(-) Compounds

Molecule 1 - FIBER PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTB
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 469008
    Fragment: FIBRE HEAD, RESIDUES 177-365
    Organism Scientific: HUMAN ADENOVIRUS 37
    Organism Taxid: 52275
    Synonym: ADENOVIRUS 37 FIBRE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
142D3Ligand/Ion3,5-DIDEOXY-5-[(METHOXYCARBONYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONICACID
2ZN3Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:312 , PRO A:317 , ASP A:318 , LYS A:345 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2004 , HOH B:2143BINDING SITE FOR RESIDUE 42D A 1
2AC2SOFTWAREHOH A:2006 , HOH A:2007 , HIS C:231BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARETYR B:312 , PRO B:317 , ASP B:318 , PRO B:320 , LYS B:345 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH C:2175BINDING SITE FOR RESIDUE 42D B 1
4AC4SOFTWAREHIS A:231 , GLU A:351 , HOH B:2006 , HOH B:2007BINDING SITE FOR RESIDUE ZN B 2
5AC5SOFTWARETYR A:308 , VAL A:322 , HOH A:2149 , TYR C:312 , PRO C:317 , ASP C:318 , LYS C:345 , HOH C:2002 , HOH C:2004 , HOH C:2005 , HOH C:2006BINDING SITE FOR RESIDUE 42D C 1
6AC6SOFTWAREHIS B:231 , GLU B:351 , HOH B:2035 , HOH C:2007BINDING SITE FOR RESIDUE ZN C 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WGU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WGU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WGU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WGU)

(-) Exons   (0, 0)

(no "Exon" information available for 2WGU)

(-) 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:185
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:185
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     
         Q64823_9ADEN   181 YDTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d2wgua_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2wguA00 A:181-365 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee.................eeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgu A 181 YDTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:183
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
         Q64823_9ADEN   183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d2wgub_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains 2wguB00 B:183-365 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee.................eeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgu B 183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   


Chain C from PDB  Type:PROTEIN  Length:183
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:183
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
         Q64823_9ADEN   183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d2wguc_ C: automated matches                                                                                                                                                            SCOP domains
               CATH domains 2wguC00 C:183-365 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                             CATH domains
           Pfam domains (1) ---Adeno_knob-2wguC01 C:186-361                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) ---Adeno_knob-2wguC02 C:186-361                                                                                                                                                    ---- Pfam domains (2)
           Pfam domains (3) ---Adeno_knob-2wguC03 C:186-361                                                                                                                                                    ---- Pfam domains (3)
         Sec.struct. author ..eee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee............hhhhheeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgu C 183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Reo_sigma (16)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q64823_9ADEN | Q64823)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

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  2wgu
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  Q64823_9ADEN | Q64823
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q64823_9ADEN | Q64823: 2j12
UniProtKB/TrEMBL
        Q64823_9ADEN | Q64823: 1uxa 1uxe 2wbw 2wgt 3n0i 3qnd 4k6t 4k6u 4k6v 4k6w 4xqa 4xqb

(-) Related Entries Specified in the PDB File

1uxa ADENOVIRUS AD37 FIBRE HEAD IN COMPLEX WITH SIALYL-LACTOSE
1uxb ADENOVIRUS AD19P FIBRE HEAD IN COMPLEX WITH SIALYL-LACTOSE
1uxe ADENOVIRUS AD37 FIBRE HEAD
2j12 AD37 FIBRE HEAD IN COMPLEX WITH CAR D1
2wgt STRUCTURE OF HUMAN ADENOVIRUS SEROTYPE 37 FIBRE HEAD IN COMPLEX WITH A SIALIC ACID DERIVATIVE, O-METHYL 5-N-PROPAONYL-3,5- DIDEOXY-D-GLYCERO-A-D-GALACTO-2- NONULOPYRANOSYLONIC ACID