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

(-) Description

Title :  PILM-PILN TYPE IV PILUS BIOGENESIS COMPLEX
 
Authors :  V. Karuppiah, J. P. Derrick
Date :  15 Mar 11  (Deposition) - 11 May 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Cycle, Type Iv Pilus Actin Secretion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Karuppiah, J. P. Derrick
Structure Of The Pilm-Piln Inner Membrane Type Iv Pilus Biogenesis Complex From Thermus Thermophilus.
J. Biol. Chem. V. 286 24434 2011
PubMed-ID: 21596754  |  Reference-DOI: 10.1074/JBC.M111.243535

(-) Compounds

Molecule 1 - COMPETENCE PROTEIN PILM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B843(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB8
 
Molecule 2 - COMPETENCE PROTEIN PILN
    Chains: B
    Fragment: RESIDUES 1-15
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB8
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , ATP A:502 , HOH A:2005 , HOH A:2049 , HOH A:2050BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLU A:19 , GLY A:21 , ALA A:22 , SER A:23 , ALA A:24 , LYS A:26 , LYS A:173 , GLY A:199 , ALA A:200 , GLU A:201 , SER A:202 , GLU A:242 , LYS A:245 , ARG A:246 , GLY A:314 , GLY A:315 , GLY A:316 , LYS A:318 , LEU A:319 , GLU A:361 , MG A:501 , HOH A:2049 , HOH A:2050 , HOH A:2052 , HOH A:2062 , HOH A:2079 , HOH A:2080 , HOH A:2081BINDING SITE FOR RESIDUE ATP A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:374 -Pro A:375

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YCH)

(-) 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:336
 aligned with Q5SIJ0_THET8 | Q5SIJ0 from UniProtKB/TrEMBL  Length:377

    Alignment length:365
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     
         Q5SIJ0_THET8    11 PRVEALGLEIGASALKLVEVSGNPPALKALASRPTPPGLLMEGMVAEPAALAQEIKELLLEARTRKRYVVTALSNLAVILRPIQVPKMPLKEMEEAVRWEAERYIPFPIDEVVLDFAPLTPLSEVQEGEQVQVMVAAARQEAVAGVLEALRGAGLVPVVLDVKPFAGLYPLEARLAEEPDRVFLALDIGAESTSLVLLRGDKPLAVRVLTLSGKDFTEAIARSFNLDLLAAEEVKRTYGMATLPTEDEELLLDFDAERERYSPGRIYDAIRPVLVELTQELRRSLEFFRIQLEEASPEVGYLLGGGSKLRGLASLLTDTLGVNFEPVNPWEAVAVDPKRFESEQLQEIGPEFAVALGLALRGVEP 375
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Competence_A-2ychA01 A:17-373                                                                                                                                                                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author .....eeeee...eeeeeeee....eeeeeeeee.....ee..ee.hhhhhhhhhhhhhhhhh....eeeeeehhhhheeeeeeee..hhhhhhhhhhhhhhhhh....-.eeeeeee..hhhhh....eeeeeeeeeehhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh....eeeeeee....eeeeeee..eeeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhh.-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh---...eeeeehhhhhh.hhhhhhhhhhh.eeee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ych A  11 PRVEALGLEIGASALKLVEVSGNPPALKALASRPTPPGLLmEGmVAEPAALAQEIKELLLEARTRKRYVVTALSNLAVILRPIQVPKmPLKEmEEAVRWEAERYIPFPI-EVVLDFAPLTPLSEVQEGEQVQVmVAAARQEAVAGVLEALRGAGLVPVVLDVKPFAGLYPLEARLAEEPDRVFLVLDIGAESTSLVLLRGDKPLAVRVLTLSGKDFTEAIARSFNLDLLAAEEVKRTYG-------------------------RIYDAIRPVLVELTQELRRSLEFFRIQL---SPEVGYLLGGGSKLRGLASLLTDTLGVNLEPVNPWEAVAVDPKRFESEQLQEIGPEFAVALGLALRGVEP 375
                                    20        30        40        50|  |    60        70        80        90       100  |    110        |-|      130       140   |   150       160       170       180       190       200       210       220       230       240        |-         -         -    |  280       290       300 |   | 310       320       330       340       350       360       370     
                                                                   51-MSE                                         98-MSE|             119 |                    144-MSE                                                                                                  249                       275                        302 306                                                                     
                                                                      54-MSE                                          103-MSE           121                                                                                                                                                                                                                                                              


Chain A from PDB  Type:PROTEIN  Length:336
 aligned with Q72IW8_THET2 | Q72IW8 from UniProtKB/TrEMBL  Length:377

    Alignment length:365
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     
         Q72IW8_THET2    11 PRVEALGLEIGASALKLVEVSGNPPALKALASRPTPPGLLMEGMVAEPAALAQEIKELLLEARTRKRYVVTALSNLAVILRPIQVPKMPLKEMEEAVRWEAERYIPFPIDEVVLDFAPLTPLSEVQEGEQVQVMVAAARQEAVAGVLEALRGAGLVPVVLDVKPFAGLYPLEARLAEEPDRVFLVLDIGAESTSLVLLRGDKPLAVRVLTLSGKDFTEAIARSFNLDLLAAEEVKRTYGMATLPTEDEELLLDFDAERERYSPGRIYDAIRPVLVELTQELRRSLEFFRIQLEEASPEMGYLLGGGSKLRGLASLLTDTLGVNFEPVNPWEAVAVDPKRFESEQLQEIGPEFAVALGLALRGVEP 375
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Competence_A-2ychA01 A:17-373                                                                                                                                                                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author .....eeeee...eeeeeeee....eeeeeeeee.....ee..ee.hhhhhhhhhhhhhhhhh....eeeeeehhhhheeeeeeee..hhhhhhhhhhhhhhhhh....-.eeeeeee..hhhhh....eeeeeeeeeehhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh....eeeeeee....eeeeeee..eeeeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhh.-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh---...eeeeehhhhhh.hhhhhhhhhhh.eeee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ych A  11 PRVEALGLEIGASALKLVEVSGNPPALKALASRPTPPGLLmEGmVAEPAALAQEIKELLLEARTRKRYVVTALSNLAVILRPIQVPKmPLKEmEEAVRWEAERYIPFPI-EVVLDFAPLTPLSEVQEGEQVQVmVAAARQEAVAGVLEALRGAGLVPVVLDVKPFAGLYPLEARLAEEPDRVFLVLDIGAESTSLVLLRGDKPLAVRVLTLSGKDFTEAIARSFNLDLLAAEEVKRTYG-------------------------RIYDAIRPVLVELTQELRRSLEFFRIQL---SPEVGYLLGGGSKLRGLASLLTDTLGVNLEPVNPWEAVAVDPKRFESEQLQEIGPEFAVALGLALRGVEP 375
                                    20        30        40        50|  |    60        70        80        90       100  |    110        |-|      130       140   |   150       160       170       180       190       200       210       220       230       240        |-         -         -    |  280       290       300 |   | 310       320       330       340       350       360       370     
                                                                   51-MSE                                         98-MSE|             119 |                    144-MSE                                                                                                  249                       275                        302 306                                                                     
                                                                      54-MSE                                          103-MSE           121                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:8
 aligned with Q5SII9_THET8 | Q5SII9 from UniProtKB/TrEMBL  Length:207

    Alignment length:8
         Q5SII9_THET8     1 MIRLNLLP   8
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2ych B   1 MIRLNLLP   8


Chain B from PDB  Type:PROTEIN  Length:8
 aligned with Q72IW7_THET2 | Q72IW7 from UniProtKB/TrEMBL  Length:207

    Alignment length:8
         Q72IW7_THET2     1 MIRLNLLP   8
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2ych B   1 MIRLNLLP   8
   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  (0, 0)

(no "SCOP Domain" information available for 2YCH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q72IW8_THET2 | Q72IW8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Chain A   (Q5SIJ0_THET8 | Q5SIJ0)

Chain B   (Q72IW7_THET2 | Q72IW7)

Chain B   (Q5SII9_THET8 | Q5SII9)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:374 - Pro A:375   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  2ych
    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
  Q5SII9_THET8 | Q5SII9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q5SIJ0_THET8 | Q5SIJ0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q72IW7_THET2 | Q72IW7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q72IW8_THET2 | Q72IW8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q5SII9_THET8 | Q5SII9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q5SIJ0_THET8 | Q5SIJ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q72IW7_THET2 | Q72IW7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q72IW8_THET2 | Q72IW8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5SII9_THET8 | Q5SII9: 4bhq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YCH)