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(-) Description

Title :  THE CRYSTAL STRUCTURE OF MOUSE TLR4/MD-2/NEOSEPTIN-3 COMPLEX
 
Authors :  Y. Wang, L. Su, M. D. Morin, B. T. Jones, L. R. Whitby, M. Surakattula, H. H H. Shi, J. H. Choi, K. Wang, E. M. Moresco, M. Berger, X. Zhan, H. Zhang, D B. Beutler
Date :  01 Mar 16  (Deposition) - 27 Apr 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  Immune Response, Protein Complex, Small Molecule Agonist, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, L. Su, M. D. Morin, B. T. Jones, L. R. Whitby, M. M. Surakattula, H. Huang, H. Shi, J. H. Choi, K. W. Wang, E. M. Moresco, M. Berger, X. Zhan H. Zhang, D. L. Boger, B. Beutler
Tlr4/Md-2 Activation By A Synthetic Agonist With No Similarity To Lps.
Proc. Natl. Acad. Sci. Usa V. 113 E884 2016
PubMed-ID: 26831104  |  Reference-DOI: 10.1073/PNAS.1525639113

(-) Compounds

Molecule 1 - TOLL-LIKE RECEPTOR 4, VARIABLE LYMPHOCYTE RECEPTOR B CHIMERA
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: TLR4 ECTODOMAIN (UNP RESIDUES 26-544) + VLRB (UNP RESIDUES 126-200)
    Gene: TLR4, LPS, VLRB
    Organism Common: MOUSE, INSHORE HAGFISH
    Organism Scientific: MUS MUSCULUS, EPTATRETUS BURGERI
    Organism Taxid: 10090, 7764
 
Molecule 2 - LYMPHOCYTE ANTIGEN 96
    Chains: C, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 19-160
    Gene: LY96, ESOP1, MD2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: LY-96, ESOP-1, PROTEIN MD-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A C 
Biological Unit 3 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric Unit (2, 27)
No.NameCountTypeFull Name
161S4Ligand/IonTERT-BUTYL (2R)-2-({4-AMINO-3-[2-(4-HYDROXYPHENYL)ETHYL]BENZOYL}AMINO)-4-PHENYLBUTANOATE
2NAG23Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 27)
No.NameCountTypeFull Name
161S4Ligand/IonTERT-BUTYL (2R)-2-({4-AMINO-3-[2-(4-HYDROXYPHENYL)ETHYL]BENZOYL}AMINO)-4-PHENYLBUTANOATE
2NAG23Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
161S1Ligand/IonTERT-BUTYL (2R)-2-({4-AMINO-3-[2-(4-HYDROXYPHENYL)ETHYL]BENZOYL}AMINO)-4-PHENYLBUTANOATE
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 15)
No.NameCountTypeFull Name
161S3Ligand/IonTERT-BUTYL (2R)-2-({4-AMINO-3-[2-(4-HYDROXYPHENYL)ETHYL]BENZOYL}AMINO)-4-PHENYLBUTANOATE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:413 , PHE A:438 , SER A:439 , VAL D:82 , PHE D:121 , PHE D:126 , PRO D:127 , 61S D:204binding site for residue 61S A 709
02AC2SOFTWARESER B:413 , PHE B:438 , SER B:439 , 61S B:711 , HOH B:863 , ILE C:52 , PHE C:121 , ILE C:124 , PRO C:127binding site for residue 61S B 710
03AC3SOFTWAREARG B:434 , GLU B:437 , 61S B:710 , HOH B:899 , ARG C:90 , PHE C:126binding site for residue 61S B 711
04AC4SOFTWAREARG A:434 , GLU A:437 , 61S A:709 , ARG D:90 , PHE D:126 , HOH D:309binding site for residue 61S D 204
05AC5SOFTWAREASN A:172 , HOH A:829binding site for Mono-Saccharide NAG A 706 bound to ASN A 172
06AC6SOFTWAREASN A:204 , HIS A:228 , ARG A:256binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 204
07AC7SOFTWAREASN A:237 , ARG A:266 , HOH A:825 , HOH A:838binding site for Mono-Saccharide NAG A 703 bound to ASN A 237
08AC8SOFTWAREASN A:307 , LYS A:329 , HOH A:883 , HOH A:922binding site for Mono-Saccharide NAG A 704 bound to ASN A 307
09AC9SOFTWAREASN A:492 , HOH A:803 , HOH A:805 , HOH A:822 , HOH A:941binding site for Mono-Saccharide NAG A 705 bound to ASN A 492
10AD1SOFTWARESER A:502 , LYS A:503 , ASN A:524 , SER A:526 , HOH A:860binding site for Poly-Saccharide residues NAG A 707 through NAG A 708 bound to ASN A 524
11AD2SOFTWARETYR A:71 , LYS B:46 , ASP B:49 , ASN B:75binding site for Poly-Saccharide residues NAG B 708 through NAG B 709 bound to ASN B 75
12AD3SOFTWAREASN B:172 , HOH B:825binding site for Mono-Saccharide NAG B 701 bound to ASN B 172
13AD4SOFTWAREASN B:204binding site for Mono-Saccharide NAG B 702 bound to ASN B 204
14AD5SOFTWAREASN B:237binding site for Mono-Saccharide NAG B 703 bound to ASN B 237
15AD6SOFTWAREASN B:307binding site for Mono-Saccharide NAG B 704 bound to ASN B 307
16AD7SOFTWARETHR B:469 , ASN B:492 , HOH B:851binding site for Mono-Saccharide NAG B 705 bound to ASN B 492
17AD8SOFTWARESER B:502 , LYS B:503 , ASN B:524 , SER B:526 , TRP B:572 , HOH B:884 , HOH B:895binding site for Poly-Saccharide residues NAG B 706 through NAG B 707 bound to ASN B 524
18AD9SOFTWAREASN C:114binding site for Mono-Saccharide NAG C 203 bound to ASN C 114
19AE1SOFTWAREASP C:38 , ARG C:132 , ASN C:150binding site for Poly-Saccharide residues NAG C 201 through NAG C 202 bound to ASN C 150
20AE2SOFTWAREGLU D:64 , ASN D:114 , HOH D:331binding site for Mono-Saccharide NAG D 201 bound to ASN D 114
21AE3SOFTWARECYS D:37 , ASP D:38 , ARG D:132 , ASN D:150 , HOH D:319binding site for Poly-Saccharide residues NAG D 202 through NAG D 203 bound to ASN D 150

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:28 -A:39
2A:280 -A:304
3A:580 -A:605
4A:582 -A:617
5B:28 -B:39
6B:280 -B:304
7B:388 -B:389
8B:580 -B:605
9B:582 -B:617
10C:25 -C:51
11C:37 -C:148
12C:95 -C:105
13D:25 -D:51
14D:37 -D:148
15D:95 -D:105

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Cys A:388 -Cys A:389
2Cys A:582 -Pro A:583
3Glu C:49 -Pro C:50
4Cys B:388 -Cys B:389
5Cys B:582 -Pro B:583
6Glu D:49 -Pro D:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IJC)

(-) 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:592
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee..................eee.......ee............eee.......ee............eee.....................eee.....................eee...........hhhhhh.....eee.......ee....hhhhhhh.....eee.......ee........eeeeeeee....hhhhhhhhhhh....eeeeeeee...........hhhhhhhhhhheeeeeee......hhhhhhhhhhh...eeeee.................eeeee................eeeee.....ee..........eee.....eeeeee.hhhhh......eee.....eeee...........eee....eeehhhhh..........eee......ee.............eee....ee...ee...........eee.......ee............eee.........hhhhhh......eee.....................eee............hhhhhhhhhhh...ee..........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ijc A  27 PCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICP 618
                                    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  


Chain B from PDB  Type:PROTEIN  Length:593
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee..................eee.......ee............eee.......ee............eee.....................eee.....................eee...........hhhhhh.....eee.......ee....hhhhhhh.....eee.......ee........eeeeeeee....hhhhhhhhhhh....eeeeeeee...........hhhhhh.....eeeeeee......hhhhhhhhhhhhh.eeeee.................eeeee................eeeee.................eee.......eeee.hhhhh......eee.....eeee...........eee....eeehhhhh..........eee......ee.............eee....ee...ee...........eee.......ee............eee.........hhhhh.......eee.....................eee............hhhhhhhhhhh...ee..........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ijc B  27 PCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT 619
                                    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   


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee........eeeee......eeeeeeeeee........eeeeeeeee..ee...eeee........hhhhhh.....eeeeeeeeee......eeeeeeeeeee....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ijc C  21 QQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAIAGDTEEKLFCLNFTIIHR 156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150      


Chain D from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeee........eeeee......eeeeeeeeee........eeeeeeeee..ee...eeee........hhhhhh.....eeeeeeeeee......eeeeeeeeeee....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ijc D  21 QQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAIAGDTEEKLFCLNFTIIHR 156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150
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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 5IJC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (87, 102)

Asymmetric Unit(hide GO term definitions)

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  5ijc
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  LY96_MOUSE | Q9JHF9
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  Q4G1L2_EPTBU | Q4G1L2
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  TLR4_MOUSE | Q9QUK6
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 Related Entries

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

UniProtKB/Swiss-Prot
        LY96_MOUSE | Q9JHF9: 2z64 3vq1 3vq2 5ijb 5ijd
        Q4G1L2_EPTBU | Q4G1L2: 2z62 2z63 2z65 2z66 2z7x 2z80 2z81 2z82
        TLR4_MOUSE | Q9QUK6: 2z64 3vq1 3vq2 5ijb 5ijd
UniProtKB/TrEMBL
        Q4G1L2_EPTBU | Q4G1L2: 2o6r 3a79 3a7b 3a7c 3ul7 3ul8 3ul9 3ula 3v44 3v47 4arn 4arr 4bv4 4qdh 4qxe 4qxf 5gy2 5ijb 5ijd

(-) Related Entries Specified in the PDB File

5ljb 5ljd