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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TLR4 POLYMORPHIC VARIANT D299G AND T399I IN COMPLEX WITH MD-2 AND LPS
 
Authors :  U. Ohto, T. Shimizu
Date :  23 Jul 12  (Deposition) - 17 Oct 12  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Leucine Rich Repeat Md-2 Related Lipid Recognition, Receptor, Innate Immunity, Lipid Binding, Glycosylation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Ohto, N. Yamakawa, S. Akashi-Takamura, K. Miyake, T. Shimizu
Structural Analyses Of Human Toll-Like Receptor 4 Polymorphisms D299G And T399I
J. Biol. Chem. V. 287 40611 2012
PubMed-ID: 23055527  |  Reference-DOI: 10.1074/JBC.M112.404608

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 4
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Cell Line: S2
    Expression System Common: FRUIT FLIES
    Expression System Taxid: 7215
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 23-629
    Gene: TLR4
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HTOLL, PROTEIN TLR4
 
Molecule 2 - LYMPHOCYTE ANTIGEN 96
    Chains: C, D
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Cell Line: S2
    Expression System Common: FRUIT FLIES
    Expression System Taxid: 7215
    Expression System Vector Type: BACULOVIRUS
    Gene: LY96, ESOP1, MD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LY-96, ESOP-1, PROTEIN MD-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1DAO2Ligand/IonLAURIC ACID
2KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3LP42Ligand/Ion2-DEOXY-3-O-[(3R)-3-HYDROXYTETRADECANOYL]-2-{[(3R)-3-HYDROXYTETRADECANOYL]AMINO}-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE
4LP52Ligand/Ion(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
5MYR2Ligand/IonMYRISTIC ACID
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:173BINDING SITE FOR RESIDUE NAG A 701
02AC2SOFTWARESER A:504 , GLN A:505 , ASN A:526 , ASP A:550 , NAG A:703 , NAG A:704 , NAG A:705BINDING SITE FOR RESIDUE NAG A 702
03AC3SOFTWARENAG A:702 , NAG A:704BINDING SITE FOR RESIDUE NAG A 703
04AC4SOFTWAREASP A:550 , SER A:552 , ASN A:575 , VAL A:602 , NAG A:702 , NAG A:703 , NAG A:705BINDING SITE FOR RESIDUE NAG A 704
05AC5SOFTWARENAG A:702 , NAG A:704BINDING SITE FOR RESIDUE NAG A 705
06AC6SOFTWARELYS B:150 , ASN B:173BINDING SITE FOR RESIDUE NAG B 701
07AC7SOFTWARESER B:504 , GLN B:505 , ASN B:526 , ASP B:550 , NAG B:703 , NAG B:704 , NAG B:705BINDING SITE FOR RESIDUE NAG B 702
08AC8SOFTWARELEU B:553 , NAG B:702 , NAG B:704 , NAG B:705BINDING SITE FOR RESIDUE NAG B 703
09AC9SOFTWARESER B:528 , ASP B:550 , SER B:552 , ASN B:575 , VAL B:602 , NAG B:702 , NAG B:703 , NAG B:705BINDING SITE FOR RESIDUE NAG B 704
10BC1SOFTWAREVAL B:548 , NAG B:702 , NAG B:703 , NAG B:704BINDING SITE FOR RESIDUE NAG B 705
11BC2SOFTWAREPHE C:64 , ASN C:114BINDING SITE FOR RESIDUE NAG C 201
12BC3SOFTWAREASN D:114BINDING SITE FOR RESIDUE NAG D 201
13BC4SOFTWAREARG A:264 , TYR A:296 , LYS A:341 , SER B:415 , GLN B:436 , GLU B:439 , PHE B:440 , ILE C:63 , TYR C:65 , PHE C:76 , LEU C:78 , VAL C:82 , LEU C:87 , ARG C:90 , TYR C:102 , ILE C:117 , SER C:118 , PHE C:119 , SER C:120 , PHE C:121 , LYS C:122 , ILE C:124 , PHE C:126 , TYR C:131 , PHE C:151BINDING SITE FOR LINKED RESIDUES C 202 TO 206
14BC5SOFTWARESER A:415 , GLN A:436 , GLU A:439 , ARG B:264 , TYR B:296 , ILE D:63 , PHE D:76 , VAL D:82 , LEU D:87 , ARG D:90 , TYR D:102 , PHE D:104 , SER D:118 , PHE D:119 , SER D:120 , PHE D:121 , LYS D:122 , ILE D:124 , PHE D:126 , TYR D:131 , PHE D:151BINDING SITE FOR LINKED RESIDUES D 202 TO 206

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:29 -A:40
2A:281 -A:306
3A:390 -A:391
4A:583 -A:609
5A:585 -A:627
6B:29 -B:40
7B:281 -B:306
8B:390 -B:391
9B:583 -B:609
10B:585 -B:627
11C:25 -C:51
12C:37 -C:148
13C:95 -C:105
14D:25 -D:51
15D:37 -D:148
16D:95 -D:105

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Cys A:390 -Cys A:391
2Glu B:27 -Pro B:28
3Cys B:390 -Cys B:391
4Thr B:611 -Pro B:612
5Asn C:49 -Pro C:50
6Asn D:49 -Pro D:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G8A)

(-) Exons   (0, 0)

(no "Exon" information available for 4G8A)

(-) 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:601
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee..................eee.......ee............eee.......ee............eee.......ee.hhhhh......eee.....................eee...........hhhhhhh....eee.......eehhhhhhhhhh......eee.......ee........eeeeeeee....hhhhhhhhhhh....eeeeeeee...............hhhhhhheeeeeeee.....eee....hhhhh...eeeee..eeeehhhhhh.....eeeee..ee............eeeee.................eee.......eeee.hhhhhh.....eee.....eeee...........eee....eee...............eee......ee.............eee....ee...ee...........eee.......ee............eee..........hhhhh......eee......................eee........hhhhhhhhhhhhhh.....hhhhh...........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8a A  27 EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDGIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTISLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITC 627
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626 


Chain B from PDB  Type:PROTEIN  Length:605
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...eee..................eee.......ee............eee.......ee............eee.......ee............eee.....................eee...........hhhhhh.....eee.......eehhhhhhhhhhh.....eee.......ee........eeeeeeee....hhhhhhhhhhh....eeeeeeee...............hhhhhhheeeeeeee.....eee....hhhhh...eeeee..eeeehhhhhh.....eeeee..ee............eeeee..ee.............eee.......eeee.hhhhhh.....eee.....eeee...........eee....eee...............eee......ee.............eee....ee...ee...........eee.......ee............eee..........hhhhh......eee..........hhhhh.......eee.....ee.hhhhhhhhhhhhhh.....hhhhh.eee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8a B  23 PESWEPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDGIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTISLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITC 627
                                    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       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622     


Chain C from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeeee........eeeee......eeeeeeeeee.........eeeeeeee..ee...eeee........hhhhhh.....eeeeeeeeee......eeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8a C  19 QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN 158
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158


Chain D from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeeee........eeeee......eeeeeeeeee.........eeeeeeee..ee...eeee........hhhhhh.....eeeeeeeeee......eeeeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8a D  19 QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN 158
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158
   Legend:   → Mismatch (orange background)
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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 4G8A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G8A)

(-) Gene Ontology  (100, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  4g8a
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  LY96_HUMAN | Q9Y6Y9
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  TLR4_HUMAN | O00206
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 Related Entries

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

UniProtKB/Swiss-Prot
        LY96_HUMAN | Q9Y6Y9: 1t2z 2e56 2e59 2z65 3fxi 3ula
        TLR4_HUMAN | O00206: 2z62 2z63 2z65 2z66 3fxi 3ul7 3ul8 3ul9 3ula

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4G8A)