Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL FRAGMENT OF ZEBRAFISH TLR5
 
Authors :  S. I. Yoon, H. Hong, I. A. Wilson
Date :  14 Dec 11  (Deposition) - 29 Feb 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym./Biol. Unit :  A
Keywords :  Flagellin, Innate Immunity, Leucine-Rich Repeat, Innate Immune Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. I. Yoon, O. Kurnasov, V. Natarajan, M. Hong, A. V. Gudkov, A. L. Osterman, I. A. Wilson
Structural Basis Of Tlr5-Flagellin Recognition And Signaling.
Science V. 335 859 2012
PubMed-ID: 22344444  |  Reference-DOI: 10.1126/SCIENCE.1215584

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 5B AND VARIABLE LYMPHOCYTE RECEPTOR B.61 CHIMERIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Taxid: 7111
    Fragment: ZEBRAFISH TOLL-LIKE RECEPTOR 5B (UNP RESIDUES 22-342) AND HAGFISH VARIABLE LYMPHOCYTE RECEPTOR B.61 (UNP RESIDUES 126-200)
    Mutation: YES
    Organism Common: ZEBRA FISH, INSHORE HAGFISH
    Organism Scientific: DANIO RERIO, EPTATRETUS BURGERI
    Organism Taxid: 7955, 7764

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:63BINDING SITE FOR RESIDUE NAG A 801
2AC2SOFTWAREASN A:89 , GLU A:112BINDING SITE FOR RESIDUE NAG A 802
3AC3SOFTWAREGLY A:196 , LYS A:197 , ASN A:228BINDING SITE FOR RESIDUE NAG A 803

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:25 -A:34
2A:187 -A:222
3A:378 -A:403
4A:380 -A:415

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:380 -Pro A:381

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V44)

(-) Exons   (0, 0)

(no "Exon" information available for 3V44)

(-) 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:401
 aligned with B3DIN1_DANRE | B3DIN1 from UniProtKB/TrEMBL  Length:875

    Alignment length:652
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               604                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             603 |                                                                      
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       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       543       553       563       573       583       593       603 |     612       622       632       642       652       662       672  
         B3DIN1_DANRE    24 VCSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLELLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIQKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFRNSSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDDAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLRNLNLTGNAVESVHTFAALPNLNKLYLGKNRISSVSSLPNIAHNLSTLDLEFNKLHALSDLYTILREFPQIENIFLQGNTFSSCYNQKQIVLSDKLQLLHLGLSSMQLIWSEEKCLNVFADLHQLQQLSLTANGLQSLPKDIFKDLTSLFFLDLSFNSLKYLPTDVFPKSLQILNLDYNSIYSVDPNLFSTLGYLSLMNNDFRCDCDLKDFQT-WLNQTNVTFVHSIEDVTCASPEDQYMVPVVRSSIQCEDEEEERRTEKLRLVLFISCTVLIILFTASTIVYI 674
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee.................eee.......ee............eee........ee............eee.......ee............eee.......hhhhhh..........eee...........hhhhhhh....eee.............hhhhh..eeeeee..............hhhhhh......eeeeee......hhhhhhhhhhhh....eeeee.......................hhhhhhh...eee.......ee............eee.......ee............eee...............----------------------------------------------------------------------------------------------------------------------------------......eee--------------------------------------------------------------------------------------............hhhhhhhhhhh--------------.....-------..........hhhh--------------h....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v44 A  24 ECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLKELALDTNQLKSVPDGIFD----------------------------------------------------------------------------------------------------------------------------------RLTSLQKIW--------------------------------------------------------------------------------------LHTNPWDCSCPRIDYLSRWLNKN--------------SQKEQ-------GSAKCSGSGKPVRS--------------IICPTSASLVPR 424
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       | -         -         -         -         -         -         -         -         -         -         -         -         -       363      |  -         -         -         -         -         -         -         -         -   |   377       387     |   -         -|   |    -  |    406     |   -         -|      422  
                                                                                                                                                                                                                                                                                                                                                                           361                                                                                                                                362     370                                                                                    371                   393            394 398     399          412            413           


Chain A from PDB  Type:PROTEIN  Length:401
 aligned with Q4G1L2_EPTBU | Q4G1L2 from UniProtKB/TrEMBL  Length:273

    Alignment length:426
                                                                                                                                                  40                                                                                                62                                                                                                                                                                                                                
                                                                                            1                19         20 23    24             39 |        50                                                                          51        61 |           75   76   81                                 82                                                                                                                                                      
                                     -         -         -         -         -         -    |    6        16  |      -   |  |  -  |     31       |40        50         -         -         -         -         -         -         -     |  55     | |64        74|    |  80|        -         -         -     |  86        96       106       116       126       136       146       156       166       176       186       196       206       216       226      
         Q4G1L2_EPTBU     - ----------------------------------------------------------------MKFALRGTCVLLALLLCCR----------NGKA-----CPSRCSCSGTEIRCNS-KGLTSVPTGIP---------------------------------------------------------------------------SSATRLELESN-KLQSLPHGVFDKLT----QLTKLS----------------------------------LSQNQIQSLPDGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPTTTTTTTTTTMPTTTTLPTTTKMSMVKVPLVPP 232
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eee.................eee.......ee............eee........ee............eee.......ee............eee.......hhhhhh..........eee...........hhhhhhh....eee.............hhhhh..eeeeee..............hhhhhh......eeeeee......hhhhhhhhhhhh....eeeee.......................hhhhhhh...eee.......ee............eee.......ee............eee.....................eee............hhhhhhhhhhh...............hhhhh....hhh-------------------------hh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v44 A  24 ECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPTSAS-------------------------LVPR 424
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413      |  -         -         -  |   
                                                                                                                                                                                                                                                                                                                                                                                                                                      420                       421
   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 3V44)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V44)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V44)

(-) Gene Ontology  (4, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4G1L2_EPTBU | Q4G1L2)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (B3DIN1_DANRE | B3DIN1)
biological process
    GO:0002253    activation of immune response    Any process that initiates an immune response.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:380 - Pro A:381   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3v44
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B3DIN1_DANRE | B3DIN1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q4G1L2_EPTBU | Q4G1L2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  B3DIN1_DANRE | B3DIN1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q4G1L2_EPTBU | Q4G1L2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q4G1L2_EPTBU | Q4G1L2: 2z62 2z63 2z65 2z66 2z7x 2z80 2z81 2z82
UniProtKB/TrEMBL
        B3DIN1_DANRE | B3DIN1: 3v47 5gy2
        Q4G1L2_EPTBU | Q4G1L2: 2o6r 3a79 3a7b 3a7c 3ul7 3ul8 3ul9 3ula 3v47 4arn 4arr 4bv4 4qdh 4qxe 4qxf 5gy2 5ijb 5ijc 5ijd

(-) Related Entries Specified in the PDB File

3v47