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(-) Description

Title :  KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12
 
Authors :  M. C. Bewley, K. Springer, Y. B. Zhang, P. Freimuth, J. M. Flanagan
Date :  05 May 99  (Deposition) - 24 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Receptor Binding, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Bewley, K. Springer, Y. B. Zhang, P. Freimuth, J. M. Flanagan
Structural Analysis Of The Mechanism Of Adenovirus Binding To Its Human Cellular Receptor, Car.
Science V. 286 1579 1999
PubMed-ID: 10567268  |  Reference-DOI: 10.1126/SCIENCE.286.5444.1579
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (FIBER KNOB PROTEIN)
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Taxid: 562
    Expression System Variant: T7
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: KNOB
    Organism Scientific: HUMAN ADENOVIRUS 12
    Organism Taxid: 28282
    Variant: SEROTYPE 12

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NOB)

(-) Sites  (0, 0)

(no "Site" information available for 1NOB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:480 -Pro A:481
2Thr B:480 -Pro B:481
3Thr C:480 -Pro C:481
4Thr D:480 -Pro D:481
5Thr E:480 -Pro E:481
6Thr F:480 -Pro F:481

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NOB)

(-) 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 A from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1noba_ A: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1nobA00 A:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee................eeeeeeeeee..eeeeeeeeee.hhhhhh......eeeeeeeee...ee..............eeee..ee......hhhhh.......hhhhh.hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nob A 403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1nobb_ B: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1nobB00 B:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee................eeeeeeeeee..eeeeeeeeee.hhhhhh.......eeeeeee....................eeee..ee......hhhhh.............hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nob B 403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1nobc_ C: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1nobC00 C:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee................eeeeeeeeee..eeeeeeeeee.hhhhh.......eeeeeeee....................eeee..ee......hhhhhh............hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhh.........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nob C 403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     


Chain D from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1nobd_ D: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1nobD00 D:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee................eee..eeeee..eeeeee.eee..hhhhh......eeeeeeee.....ee.............eeee..ee........................hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nob D 403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     


Chain E from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1nobe_ E: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1nobE00 E:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee................eeeeeeeeee..eeeeeeeeee.hhhhh.......eeeeeeee....................eeee..ee......hhhhh.......hhhhh.hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhh.........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nob E 403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     


Chain F from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1nobf_ F: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1nobF00 F:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee................eeeeeeeeee..eeeeeeeeee.hhhhhh......eeeeeeee....................eeee..ee......hhhhhh............hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nob F 403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NOB)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (SPIKE_ADE12 | P36711)
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:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    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:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_ADE12 | P36711: 1kac 1p69 1p6a

(-) Related Entries Specified in the PDB File

1kac