Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF YERSINIA PESTIS YSCU N263A MUTANT
 
Authors :  G. T. Lountos, B. P. Austin, S. Nallamsetty, D. S. Waugh
Date :  09 Sep 08  (Deposition) - 03 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cell Membrane, Transmembrane, Yersinia Pestis, Molecular Switch, Protein Transport, Atomic Resolution, Membrane, Virulence, Transport, Type Iii Secretion System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. T. Lountos, B. P. Austin, S. Nallamsetty, D. S. Waugh
Atomic Resolution Structure Of The Cytoplasmic Domain Of Yersinia Pestis Yscu, A Regulatory Switch Involved In Type Iii Secretion.
Protein Sci. V. 18 467 2009
PubMed-ID: 19165725  |  Reference-DOI: 10.1002/PRO.56

(-) Compounds

Molecule 1 - YOP PROTEINS TRANSLOCATION PROTEIN U
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBA2086
    Expression System Taxid: 562
    Fragment: CYTOPLASMIC DOMAIN, RESIDUES 211-354
    Mutation: YES
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: YSCU

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
11PE8Ligand/IonPENTAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:243 , THR A:288 , ASP A:289 , GLN A:291 , TYR A:317BINDING SITE FOR RESIDUE 1PE A1345
2AC2SOFTWAREARG A:248 , ASN A:249 , MET A:250 , ARG A:251 , TYR A:287BINDING SITE FOR RESIDUE 1PE A1346
3AC3SOFTWAREILE A:306 , LEU A:307 , HOH A:2060 , HOH A:2128BINDING SITE FOR RESIDUE 1PE A1347
4AC4SOFTWAREARG A:309 , ILE A:310 , PRO A:311 , LEU A:312 , ALA A:315 , GLN A:330 , ALA A:333 , HOH A:2063 , HOH A:2102 , HOH A:2129BINDING SITE FOR RESIDUE 1PE A1348

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:275 -Gly A:276
2Gly A:276 -Glu A:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JLH)

(-) Exons   (0, 0)

(no "Exon" information available for 2JLH)

(-) 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:114
 aligned with YSCU_YERPE | P69986 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:114
                                   240       250       260       270       280       290       300       310       320       330       340    
           YSCU_YERPE   231 SPEIKSKRRQFHQEIQSRNMRENVKRSSVVVANPTHIAIGILYKRGETPLPLVTFKYTDAQVQTVRKIAEEEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVLRWLERQ 344
               SCOP domains d2jlha_ A: automated matches                                                                                       SCOP domains
               CATH domains 2jlhA00 A:231-344 secretion proteins EscU                                                                          CATH domains
               Pfam domains Bac_export_2-2jlhA01 A:231-342                                                                                  -- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhh..eeeee...eeeeee.........eeeeeee.hhhhhhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2jlh A 231 SPEIKSKRRQFHQEIQSRNMRENVKRSSVVVAAPTHIAIGILYKRGETPLPLVTFKYTDAQVQTVRKIAEEEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVLRWLERQ 344
                                   240       250       260       270       280       290       300       310       320       330       340
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Bac_export_2] (5)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (YSCU_YERPE | P69986)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:275 - Gly A:276   [ RasMol ]  
    Gly A:276 - Glu A:277   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2jlh
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  YSCU_YERPE | P69986
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  YSCU_YERPE | P69986
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        YSCU_YERPE | P69986: 2jli 2jlj

(-) Related Entries Specified in the PDB File

2jli ATOMIC RESOLUTION STRUCTURE OF THE CYTOPLASMIC DOMAIN OF YERSINIA PESTIS YSCU, A REGULATORY SWITCH INVOLVED IN TYPE III SECRETION
2jlj CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF YERSINIA PESTIS YSCU N263A P264A MUTANT