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(-) Description

Title :  CRYSTAL STRUCTURE OF INTERNALIN B (INLB), A LISTERIA MONOCYTOGENES VIRULENCE PROTEIN CONTAINING SH3-LIKE DOMAINS.
 
Authors :  M. Marino, M. Banerjee, R. Jonquieres, P. Cossart, P. Ghosh
Date :  29 Jul 02  (Deposition) - 06 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Internalin, Cell Invasion, Gw Domains, Sh3 Domains, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Marino, M. Banerjee, R. Jonquieres, P. Cossart, P. Ghosh
Gw Domains Of The Listeria Monocytogenes Invasion Protein Inlb Are Sh3-Like And Mediate Binding To Host Ligands
Embo J. V. 21 5623 2002
PubMed-ID: 12411480  |  Reference-DOI: 10.1093/EMBOJ/CDF558
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERNALIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: T7
    Expression System Vector Type: PLASMID
    Gene: INLB
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2TB7Ligand/IonTERBIUM(III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:150 , ASN A:173 , GLU A:194 , HOH A:688BINDING SITE FOR RESIDUE TB A 639
2AC2SOFTWAREGLU A:150BINDING SITE FOR RESIDUE TB A 641
3AC3SOFTWAREASP A:275BINDING SITE FOR RESIDUE TB A 642
4AC4SOFTWAREPRO A:49 , ASP A:51BINDING SITE FOR RESIDUE TB A 644
5AC5SOFTWAREASN A:231 , ASP A:233BINDING SITE FOR RESIDUE TB A 645
6AC6SOFTWAREARG A:515 , ARG A:584BINDING SITE FOR RESIDUE SO4 A 646

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M9S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M9S)

(-) PROSITE Motifs  (2, 9)

Asymmetric/Biological Unit (2, 9)
 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
2GWPS51780 GW domain profile.INLB_LISMO393-467
472-550
553-630		  3A:393-467
A:472-550
A:553-629

(-) Exons   (0, 0)

(no "Exon" information available for 1M9S)

(-) 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:523
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:594
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625    
           INLB_LISMO    36 ETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKEVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAETTEKAVNLTRYVKYIRGNAGIYKLPREDNSLKQGTLASHRCKALTVDREARNGGKLWYRLKNIGWTKAENLSLDRYDKMEYDKGVTAYARVRNASGNSVWTKPYNTAGAKHVNKLSVYQGKNMRILREAKTPITTWYQFSIGGKVIGWVDTRALNTFYKQSMEKPTRLTRYVSANKAGESYYKVPVADNPVKRGTLAKYKNQKLIVDCQATIEGQLWYRIRTSSTFIGWTKAANLRAQ 629
               SCOP domains d1m9sa5 A:36-240 Internalin B                                                                                                                                                                                d1m9sa1 A:241-319 Internalin B                                                 -----------------------------------------------------------------------d1m9sa2 A:391-465 Internalin B, C-terminal domains                         d1m9sa3 A:466-551 Internalin B, C-terminal domains                                    d1m9sa4 A:552-629 Internalin B, C-terminal domains                             SCOP domains
               CATH domains 1m9sA01 A:36-240 Ribonuclease Inhibitor                                                                                                                                                                      1m9sA02 A:241-319  [code=2.60.40.1220, no name defined]                        -----------------------------------------------------------------------1m9sA03 A:391-465  [code=2.30.30.170, no name defined]                     1m9sA04 A:466-551  [code=2.30.30.170, no name defined]                                1m9sA05 A:552-629  [code=2.30.30.170, no name defined]                         CATH domains
           Pfam domains (1) Internalin_N-1m9sA07    --------------------------------------------------------------------------------------------------------LRR_4-1m9sA01 A:164-206                    LRR_6-1m9sA03 A:207-233    ------------------------------LRR_adjacent-1m9sA08 A:264-319                          -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SH3_8-1m9sA04 A:553-627                                                    -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------LRR_4-1m9sA02 A:164-206                    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SH3_8-1m9sA05 A:553-627                                                    -- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SH3_8-1m9sA06 A:553-627                                                    -- Pfam domains (3)
         Sec.struct. author ......eehhhhh.hhhhhhhhhhhh.......eehhhhhh................hhhhh....eee........hhhhhhh....eee...................eee........hhhhhhh....eee........hhhhhh.....eee........hhhhh......eee........hhhhh......eee...eeee..........eee..............ee....eee..eee........eeeeeeeeeeee..eeeeeeeeeeee.-----------------------------------------------------------------------....................eee.....hhh.eeee.....................eee.....eee...................eeeee......ee............eee.hhhh...eee...ee....eeeeeee..eeeeeee...eeeeee.hhheeeeeeeee.......eee.....hhh.eeee.hhh....eeeeeeeee..eeeeeee....eeeeee...ee.. 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   ------------------------------------------------------------------------------------------------------------------------------------------------------------------GW  PDB: A:393-467 UniProt: 393-467                                        ----GW  PDB: A:472-550 UniProt: 472-550                                            --GW  PDB: A:553-629 UniProt: 553-630                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1m9s A  36 ETITVSTPIKQIFPDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLTNLKNLGWLFLDENKIKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPL-----------------------------------------------------------------------ETTEKTVNLTRYVKYIRGNAGIYKLPREDNSLKQGTLASHRCKALTVDREARNGGKLWYRLKNIGWTKAENLSLDRYDKMEYDKGVTAYARVRNASGNSVWTKPYNTAGAKHVNKLSVYQGKNMRILREAKTPITTWYQFSIGGKVIGWVDTRALNTFYKQSMEKPTRLTRYVSANKAGESYYKVPVADNPVKRGTLAKYKNQKLIVDCQATIEGQLWYRIRTSSTFIGWTKAANLRAQ 629
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315   |     -         -         -         -         -         -         -     | 395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625    
                                                                                                                                                                                                                                                                                                                     319                                                                     391
   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  (3, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (5, 8)

Asymmetric/Biological Unit
(-)
Clan: LRR (77)
(-)
Clan: SH3 (175)
(-)
Family: SH3_8 (1)
(-)
Listeria monocytogenes (1)
3aSH3_8-1m9sA04A:553-627
3bSH3_8-1m9sA05A:553-627
3cSH3_8-1m9sA06A:553-627
(-)
Clan: no clan defined [family: Internalin_N] (18)
(-)
Clan: no clan defined [family: LRR_adjacent] (15)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological 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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  1m9s
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 Related Entries

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

UniProtKB/Swiss-Prot
        INLB_LISMO | P25147: 1d0b 1h6t 1otm 1otn 1oto 2uzx 2uzy 2wqu 2wqv 2wqw 2wqx 2y5p 2y5q 4aw4 4cil

(-) Related Entries Specified in the PDB File

1cka C-CRK SH3 DOMAIN
1d0b INTERNALIN B LRR DOMAIN
1h6t INTERNALIN B RBD DOMAIN
1h6u INTERNALIN H RBD-LIKE DOMAIN
2abl ABL SH3 DOMAIN