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(-) Description

Title :  LISTERIA MONOCYTOGENES INLB (INTERNALIN B) RESIDUES 36-392
 
Authors :  M. Ebbes, H. H. Niemann
Date :  17 Jan 11  (Deposition) - 23 Feb 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Protein Binding, Leucine Rich Repeat, Virulence Factor, Pathogenicity Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ebbes, W. M. Bleymuller, M. Cernescu, R. Nolker, B. Brutschy, H. H. Niemann
Fold And Function Of The Inlb B-Repeat.
J. Biol. Chem. V. 286 15496 2011
PubMed-ID: 21345802  |  Reference-DOI: 10.1074/JBC.M110.189951

(-) Compounds

Molecule 1 - INTERNALIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: CODON PLUS
    Expression System Vector: PGEX-6P-1
    Expression System Vector Type: PLASMID
    Fragment: INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Other Details: THE B-REPEAT (RESIDUES 322-392) IS NOT VISIBLE IN THE ELECTRON DENSITY.
    Strain: EGD
    Synonym: INLB

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:55 , ASP A:59 , HIS A:162BINDING SITE FOR RESIDUE ZN A1322
2AC2SOFTWAREGLU A:270 , HIS A:312BINDING SITE FOR RESIDUE ZN A1323
3AC3SOFTWAREGLU A:129 , HIS A:151 , ASP A:275 , HIS A:286BINDING SITE FOR RESIDUE ZN A1324

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y5Q)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:280 -Pro A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y5Q)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.INLB_LISMO99-120
121-142
143-164
165-186
187-208
209-230		  6A:99-120
A:121-142
A:143-164
A:165-186
A:187-208
A:209-230
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.INLB_LISMO99-120
121-142
143-164
165-186
187-208
209-230		  6A:99-120
A:121-142
A:143-164
A:165-186
A:187-208
A:209-230
Biological Unit 2 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.INLB_LISMO99-120
121-142
143-164
165-186
187-208
209-230		  12A:99-120
A:121-142
A:143-164
A:165-186
A:187-208
A:209-230

(-) Exons   (0, 0)

(no "Exon" information available for 2Y5Q)

(-) 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:289
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:295
                                    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     
           INLB_LISMO    27 IGNGAKVQAETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Internalin_N-2y5qA04    --------------------------------------------------------------------------------------------------------LRR_4-2y5qA01 A:164-206                    LRR_6-2y5qA03 A:207-233    ------------------------------LRR_adjacent-2y5qA05 A:264-321                             Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------LRR_4-2y5qA02 A:164-206                    ------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..------.......eehhhhh.hhhhhhhhhhhh.......eehhhhhhh..eee..........hhhhh....eee........hhhhh......eee.......hhhhhhhh....eee........hhhhhhh....eee........hhhhhhh....eee........hhhhh......eee........hhhhh......eee...eee....ee.....eee............eeee....eee..eee........eeeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------LRR  PDB: A:99-120    LRR  PDB: A:121-142   LRR  PDB: A:143-164   LRR  PDB: A:165-186   LRR  PDB: A:187-208   LRR  PDB: A:209-230   ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5q A  33 LG------SETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKE 321
                             |      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     
                             |     35                                                                                                                                                                                                                                                                                              
                            34
   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 2Y5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y5Q)

(-) Pfam Domains  (4, 5)

Asymmetric Unit
(-)
Clan: LRR (77)
(-)
Clan: no clan defined [family: Internalin_N] (18)
(-)
Clan: no clan defined [family: LRR_adjacent] (15)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (INLB_LISMO | P25147)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

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    Lys A:280 - Pro A:281   [ RasMol ]  
 
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  2y5q
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  INLB_LISMO | P25147
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 Related Entries

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

UniProtKB/Swiss-Prot
        INLB_LISMO | P25147: 1d0b 1h6t 1m9s 1otm 1otn 1oto 2uzx 2uzy 2wqu 2wqv 2wqw 2wqx 2y5p 4aw4 4cil

(-) Related Entries Specified in the PDB File

1d0b INTERNALIN B LEUCINE RICH REPEAT DOMAIN
1h6t INTERNALIN B: CRYSTAL STRUCTURE OF FUSED N-TERMINAL DOMAINS.
1m9s CRYSTAL STRUCTURE OF INTERNALIN B (INLB), A LISTERIAMONOCYTOGENES VIRULENCE PROTEIN CONTAINING SH3- LIKEDOMAINS.
1otm CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1otn CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1oto CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
2uzx STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: CRYSTAL FORM I
2uzy STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: LOW RESOLUTION, CRYSTAL FORM II
2wqu INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: TRICLINIC CRYSTAL FORM
2wqv INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: RHOMBOHEDRAL CRYSTAL FORM
2wqw DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN
2wqx INLB321_4R: S199R, D200R, G206R, A227R, C242A MUTANT OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN
2y5p B-REPEAT OF LISTERIA MONOCYTOGENES INLB (INTERNALIN B)