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(-) Description

Title :  ADENOVIRUS AD19P FIBRE HEAD IN COMPLEX WITH SIALYL-LACTOSE
 
Authors :  W. P. Burmeister, D. Guilligay, S. Cusack, G. Wadell, N. Arnberg
Date :  24 Feb 04  (Deposition) - 01 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Viral Protein, Adenovirus, Ad19P, Fibre, Receptor, Sialic Acid, Neuraminic Acid, Cd46, Daf, Conjunctivitis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. P. Burmeister, D. Guilligay, S. Cusack, G. Wadell, N. Arnberg
Crystal Structure Of Species D Adenovirus Fiber Knobs And Their Sialic Acid Binding Sites
J. Virol. V. 78 7727 2004
PubMed-ID: 15220447  |  Reference-DOI: 10.1128/JVI.78.14.7727-7736.2004

(-) Compounds

Molecule 1 - FIBER PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: HEAD DOMAIN, RESIDUES 172-365
    Mutation: YES
    Organism Scientific: HUMAN ADENOVIRUS TYPE 19
    Organism Taxid: 28278
    Other Details: ONLY THE KNOB DOMAIN, AFTER TEV CLEAVAGE OF A HIS-TAGGED PROTEIN CONSTRUCT
    Strain: P

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GAL3Ligand/IonBETA-D-GALACTOSE
3SIA3Ligand/IonO-SIALIC ACID
4ZN3Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:312 , PRO A:317 , ASP A:318 , LYS A:345 , GAL A:1368 , HOH A:2154 , HOH A:2173 , HOH A:2174 , HOH A:2175 , TYR B:308 , VAL B:322 , SER B:344 , HOH B:2111 , HOH B:2144BINDING SITE FOR RESIDUE SIA A1366
02AC2SOFTWARESIA A:1366 , HOH A:2178 , HOH C:2229BINDING SITE FOR RESIDUE GAL A1368
03AC3SOFTWARETYR B:312 , PRO B:317 , ASP B:318 , PRO B:320 , LYS B:345 , GAL B:1368 , HOH B:2168 , HOH B:2169 , HOH B:2170 , HOH B:2171 , HOH B:2172 , HOH B:2176 , TYR C:308 , VAL C:322 , HOH C:2147 , HOH C:2191BINDING SITE FOR RESIDUE SIA B1366
04AC4SOFTWARESIA B:1366 , HOH B:2176 , HOH B:2177 , HOH C:2194BINDING SITE FOR RESIDUE GAL B1368
05AC5SOFTWARETYR A:308 , HOH A:2114 , HOH A:2152 , TYR C:312 , PRO C:317 , ASP C:318 , PRO C:320 , LYS C:345 , GAL C:1368 , HOH C:2217 , HOH C:2218 , HOH C:2219 , HOH C:2220 , HOH C:2221 , HOH C:2222 , HOH C:2223 , HOH C:2224BINDING SITE FOR RESIDUE SIA C1367
06AC6SOFTWARESIA C:1367 , HOH C:2217 , HOH C:2221 , HOH C:2225 , HOH C:2226 , HOH C:2228 , HOH C:2229 , HOH C:2230BINDING SITE FOR RESIDUE GAL C1368
07AC7SOFTWAREHIS A:231 , GLU A:351 , ACT A:1369 , ACT A:1370 , HOH A:2177 , HOH A:2179BINDING SITE FOR RESIDUE ZN A1367
08AC8SOFTWAREVAL A:226 , HIS A:231 , GLU A:351 , ZN A:1367 , ACT A:1370 , HOH A:2177 , HOH A:2179 , LYS B:300 , TYR B:302BINDING SITE FOR RESIDUE ACT A1369
09AC9SOFTWAREHIS A:231 , GLU A:351 , ZN A:1367 , ACT A:1369 , HOH A:2179BINDING SITE FOR RESIDUE ACT A1370
10BC1SOFTWAREHIS B:231 , GLU B:351 , HOH B:2173 , HOH B:2174 , HOH B:2175BINDING SITE FOR RESIDUE ZN B1367
11BC2SOFTWAREHIS C:231 , ACT C:1369BINDING SITE FOR RESIDUE ZN C1366
12BC3SOFTWAREHIS C:231 , ILE C:232 , GLU C:351 , ZN C:1366 , HOH C:2202BINDING SITE FOR RESIDUE ACT C1369

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UXB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UXB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UXB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UXB)

(-) Exons   (0, 0)

(no "Exon" information available for 1UXB)

(-) 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:184
 aligned with Q64822_9ADEN | Q64822 from UniProtKB/TrEMBL  Length:365

    Alignment length:184
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q64822_9ADEN   182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d1uxba_ A: Adenovirus fiber protein knob domain                                                                                                                                          SCOP domains
               CATH domains 1uxbA00 A:182-365 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 1uxb A 182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE 365
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with Q64822_9ADEN | Q64822 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   
         Q64822_9ADEN   183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d1uxbb_ B: Adenovirus fiber protein knob domain                                                                                                                                         SCOP domains
               CATH domains 1uxbB00 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
                 1uxb B 183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE 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 Q64822_9ADEN | Q64822 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   
         Q64822_9ADEN   183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d1uxbc_ C: Adenovirus fiber protein knob domain                                                                                                                                         SCOP domains
               CATH domains 1uxbC00 C:183-365 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                             CATH domains
           Pfam domains (1) ---Adeno_knob-1uxbC01 C:186-361                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) ---Adeno_knob-1uxbC02 C:186-361                                                                                                                                                    ---- Pfam domains (2)
           Pfam domains (3) ---Adeno_knob-1uxbC03 C:186-361                                                                                                                                                    ---- Pfam domains (3)
         Sec.struct. author ..eeee...............eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee............hhh.eeeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uxb C 183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE 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  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q64822_9ADEN | Q64822)
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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(-) Related Entries Specified in the PDB File

1uxa THE CRYSTAL STRUCTURE OF ADENOVIRUS AD37 FIBRE HEAD IN COMPLEX WITH SIALYL-LACTOSE
1uxe THE CRYSTAL STRUCTURE OF ADENOVIRUS AD37 FIBRE HEAD