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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF MOUSE TLR9
 
Authors :  B. C. Collins, I. A. Wilson
Date :  13 May 14  (Deposition) - 11 Jun 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosylation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Collins, I. A. Wilson
Crystal Structure Of The C-Terminal Domain Of Mouse Tlr9.
Proteins V. 82 2874 2014
PubMed-ID: 24888966  |  Reference-DOI: 10.1002/PROT.24616

(-) Compounds

Molecule 1 - VARIABLE LYMPHOCYTE RECEPTOR B, TOLL-LIKE RECEPTOR 9 CHIMERA
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: SEE REMARK 999
    Gene: TLR9, VLRB
    Organism Common: INSHORE HAGFISH, MOUSE
    Organism Scientific: EPTATRETUS BURGERI, MUS MUSCULUS
    Organism Taxid: 7764, 10090
    Synonym: INNATE IMMUNE RECEPTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:173 , HIS A:174 , HOH A:603BINDING SITE FOR RESIDUE SO4 A 506
02AC2SOFTWAREHIS A:117 , TRP A:118 , ASN A:147BINDING SITE FOR RESIDUE SO4 A 507
03AC3SOFTWARESER A:87 , LYS A:112 , SER B:290BINDING SITE FOR RESIDUE SO4 A 508
04AC4SOFTWAREHIS A:164 , HOH A:607 , TYR B:244BINDING SITE FOR RESIDUE SO4 A 509
05AC5SOFTWARESER B:172 , SER B:173 , NAG B:502BINDING SITE FOR RESIDUE SO4 B 506
06AC6SOFTWAREHIS B:117 , TRP B:118 , ASN B:147 , HOH B:618 , HOH B:652BINDING SITE FOR RESIDUE SO4 B 507
07AC7SOFTWARESER A:290 , SER B:87 , LYS B:112BINDING SITE FOR RESIDUE SO4 B 508
08AC8SOFTWARETYR A:244 , HIS B:164 , GLY B:187 , HOH B:614BINDING SITE FOR RESIDUE SO4 B 509
09AC9SOFTWAREGLN A:90 , ALA A:91 , ASN A:93 , GLN A:96BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 93
10BC1SOFTWARETRP A:118 , ASN A:147 , SER A:149 , SER A:172BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 147
11BC2SOFTWAREPRO A:225 , PHE A:247 , ASN A:249 , PHE A:255 , HOH A:655BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 249
12BC3SOFTWAREPHE A:247 , ASN A:274BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 274
13BC4SOFTWARESER A:289 , SER A:290 , ASN A:311 , TRP A:360 , HOH A:623BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 311
14BC5SOFTWAREGLN B:90 , ALA B:91 , ASN B:93 , GLN B:96 , HOH B:609BINDING SITE FOR MONO-SACCHARIDE NAG B 501 BOUND TO ASN B 93
15BC6SOFTWARETRP B:118 , ASN B:147 , SER B:149 , SO4 B:506BINDING SITE FOR MONO-SACCHARIDE NAG B 502 BOUND TO ASN B 147
16BC7SOFTWAREPRO B:225 , ASN B:249 , ASN B:274BINDING SITE FOR MONO-SACCHARIDE NAG B 503 BOUND TO ASN B 249
17BC8SOFTWAREPHE B:247 , ASN B:274BINDING SITE FOR MONO-SACCHARIDE NAG B 504 BOUND TO ASN B 274
18BC9SOFTWARESER B:289 , SER B:290 , ASN B:311 , HIS B:314 , TRP B:360 , HOH B:617BINDING SITE FOR MONO-SACCHARIDE NAG B 505 BOUND TO ASN B 311

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:1 -A:7
2A:5 -A:14
3A:368 -A:393
4A:370 -A:405
5B:1 -B:7
6B:5 -B:14
7B:368 -B:393
8B:370 -B:405

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QDH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QDH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QDH)

(-) Exons   (0, 0)

(no "Exon" information available for 4QDH)

(-) 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:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee..eee..................eee.....................eee.........hhhhhh......eee......................eee.....................eee.............hhhhhh....eee..............ee....eee....hhhhhhhh.........ee....eee.........hhhhhhh......eee.........hhhhhhhh....eee.....................eee.....................eee................hhhhh.eee.....................eee........hhhhhhhhhhhhhhh...ee..........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qdh A   1 CPSRCSCSGTEIRCNSKGLTSVPTGIPSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSRNNLVTIKPEMFVNLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFIGHNFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTNGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMNLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICP 406
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404  
                                                                                                                                                                    139|                                                                                                                                                                                                                                                                      
                                                                                                                                                                     144                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee..................eee.....................eee.........hhhhhh......eee......................eee.....................eee.............hhhhhh....eee..............ee....eee....hhhhhhhh.........ee....eee.........hhhhhhh......eee.........hhhhhhhh....eee.......ee............eee.......ee............eee...............eee...................eee........hhhhhhhhhhhhhhh...ee..........hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdh B   1 CPSRCSCSGTEIRCNSKGLTSVPTGIPSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSRNNLVTIKPEMFVNLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFIGHNFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTNGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWLKELALDTNQLKSVPDGIFDTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICP 406
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324|      341       351|      363       373       383       393       403   
                                                                                                                                                                    139|                                                                                                                                                                                 324|                351|                                                    
                                                                                                                                                                     144                                                                                                                                                                                  332                 354
   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 4QDH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QDH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QDH)

(-) Gene Ontology  (65, 67)

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  4qdh
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  TLR9_MOUSE | Q9EQU3
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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
        TLR9_MOUSE | Q9EQU3: 3wpf 3wpg 3wph 3wpi
UniProtKB/TrEMBL
        Q4G1L2_EPTBU | Q4G1L2: 2o6r 3a79 3a7b 3a7c 3ul7 3ul8 3ul9 3ula 3v44 3v47 4arn 4arr 4bv4 4qxe 4qxf 5gy2 5ijb 5ijc 5ijd

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