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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX BETWEEN BACILLUS SUBTILIS FLAGELLIN AND ZEBRAFISH TOLL-LIKE RECEPTOR 5
 
Authors :  W. S. Song, S. I. Yoon
Date :  21 Sep 16  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Bacterial Protein Immune Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Song, Y. J. Jeon, B. Namgung, M. Hong, S. I. Yoon
A Conserved Tlr5 Binding And Activation Hot Spot On Flagellin
Sci Rep V. 7 40878 2017
PubMed-ID: 28106112  |  Reference-DOI: 10.1038/SREP40878

(-) Compounds

Molecule 1 - TLR5B PROTEIN,VARIABLE LYMPHOCYTE RECEPTOR B
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: TLR5B, VLRB
    Mutation: YES
    Organism Common: ZEBRAFISH, INSHORE HAGFISH
    Organism Scientific: DANIO RERIO, EPTATRETUS BURGERI
    Organism Taxid: 7955, 7764
    Other Details: FUSION PROTEIN OF TLR5B (B3DIN1, UNP RESIDUES 23-390) AND VARIABLE LYMPHOCYTE RECEPTOR B (Q4G1L2, UNP RESIDUES 126-200)
    Synonym: TOLL-LIKE RECEPTOR 5B
 
Molecule 2 - FLAGELLIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 54-230
    Gene: HAG, BSUW23_17335
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SPIZIZENII STRAIN W23
    Organism Taxid: 655816
    Strain: W23

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:329 , ASN A:374 , HIS A:375 , ARG A:377 , GLN A:399 , HOH A:967binding site for residue PG4 A 806
02AC2SOFTWAREASN B:329 , ASN B:374 , HIS B:375 , ARG B:377 , GLN B:399binding site for residue PG4 B 806
03AC3SOFTWAREASN A:63 , GLU A:64 , THR A:65binding site for Mono-Saccharide NAG A 801 bound to ASN A 63
04AC4SOFTWAREASN A:89 , GLU A:112 , THR A:113binding site for Mono-Saccharide NAG A 802 bound to ASN A 89
05AC5SOFTWAREASN A:228binding site for Mono-Saccharide NAG A 803 bound to ASN A 228
06AC6SOFTWAREALA A:324 , GLN A:325 , LYS A:344 , ASN A:346 , GLN A:349 , ASP A:370 , HOH A:973binding site for Poly-Saccharide residues NAG A 804 through NAG A 805 bound to ASN A 346
07AC7SOFTWAREASN B:63binding site for Mono-Saccharide NAG B 801 bound to ASN B 63
08AC8SOFTWAREASN B:89 , GLU B:112 , THR B:113 , HOH B:907binding site for Mono-Saccharide NAG B 802 bound to ASN B 89
09AC9SOFTWAREASN B:228binding site for Mono-Saccharide NAG B 803 bound to ASN B 228
10AD1SOFTWAREALA B:324 , ASN B:346 , GLN B:349 , VAL B:368 , ASP B:370 , HOH B:1028binding site for Poly-Saccharide residues NAG B 804 through NAG B 805 bound to ASN B 346

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:25 -A:34
2A:187 -A:222
3A:426 -A:451
4A:428 -A:463
5B:25 -B:34
6B:187 -B:222
7B:426 -B:451
8B:428 -B:463

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Cys A:428 -Pro A:429
2Cys B:428 -Pro B:429

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GY2)

(-) Exons   (0, 0)

(no "Exon" information available for 5GY2)

(-) 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:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               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...eeeeee.......................hhhhhhh...eee.......ee............eee.......ee............eee.....................eee.....................eee.....................eee............hhhhhhhhhhh...............hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gy2 A  23 SECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICP 464
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  


Chain B from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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............hhhhhhh.......eeeeee......hhhhhhhhhhhh...eeeeee.......................hhhhhhh...eee.......ee............eee.......ee............eee.....................eee.....................eee.....................eee............hhhhhhhhhhh...............hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gy2 B  24 ECSVIGYNAICINRGLHQVPELPAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICP 464
                                    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 


Chain C from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhee..ee..........eeee.......eeee.....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gy2 C  54 GQIRGLEMASKNSQDGISLIQTAEGALTETHAILQRMRELTVQAGNTGTQQAEDLGAIKDEMDALIEEIDGISNRTEFNGKKLLDGTNSTDGFTFQIGANAGQQLNVKIDSMSSTALGVNALDVTDFAATAFDDQLKSIDTAINTVSTQRAKLGAVQNRLEHTINNLGA 222
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         


Chain D from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhee..ee..........eeee.......eeee.....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gy2 D  54 GQIRGLEMASKNSQDGISLIQTAEGALTETHAILQRMRELTVQAGNTGTQQAEDLGAIKDEMDALIEEIDGISNRTEFNGKKLLDGTNSTDGFTFQIGANAGQQLNVKIDSMSSTALGVNALDVTDFAATAFDDQLKSIDTAINTVSTQRAKLGAVQNRLEHTINNLGA 222
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5GY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GY2)

(-) Gene Ontology  (9, 11)

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 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: 3v44 3v47
        Q4G1L2_EPTBU | Q4G1L2: 2o6r 3a79 3a7b 3a7c 3ul7 3ul8 3ul9 3ula 3v44 3v47 4arn 4arr 4bv4 4qdh 4qxe 4qxf 5ijb 5ijc 5ijd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GY2)