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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE ALA9VAL, ALA11VAL, AND LEU13VAL MUTATIONS IN THE GD DONOR STRAND
 
Authors :  L. J. Fooks, X. Yu, E. Moslehi-Mohebi, V. Tischenko, S. D. Knight, S. Macintyre, A. V. Zavialov
Date :  07 Jul 08  (Deposition) - 14 Jul 09  (Release) - 14 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Donor Strand Complementation, Fimbriae, Chaperone, Protein- Protein Complex, Beta Barrel, Immunoglobulin Domain, Periplasm, Plasmid, Capsule, Secreted, Chaperone/Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Fooks, X. Yu, E. Moslehi-Mohebi, V. Tischenko, S. D. Knight, S. Macintyre, A. V. Zavialov
Hydrophobicity And Rigidity Of Binding Segments Enable Caf1M Chaperone To Act As Assembly Catalyst
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN CAF1M
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 24 TO 258
    GeneCAF1M, YPMT1.82, Y5194, Y1098, YP_PMT084
    Organism ScientificYERSINIA PESTIS
    Organism Taxid632
    SynonymCAPSULE PROTEIN FRACTION 1 MACHINERY
 
Molecule 2 - F1 CAPSULE ANTIGEN
    ChainsB, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES22 TO 170
    GeneCAF1, YPMT1.84, Y5196, Y1100, YP_PMT082
    MutationYES
    Organism ScientificYERSINIA PESTIS
    Organism Taxid632

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DPB)

(-) Sites  (0, 0)

(no "Site" information available for 3DPB)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:98 -A:137

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:64 -Pro A:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DPB)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.CAF1M_YERPE110-127  1A:87-104

(-) Exons   (0, 0)

(no "Exon" information available for 3DPB)

(-) 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:196
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:226
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
          CAF1M_YERPE    32 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVT 257
               SCOP domains d3dpba1 A:9-147 Chaperone protein Caf1m                                                                                                    d3dpba2 A:148-234 Caf1m                                                                 SCOP domains
               CATH domains -----3dpbA01 A:14-145 PapD-like                                                                                                          ---3dpbA02 A:149-232  [code=2.60.40.1070, no name defined]                             -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeee....eeeeeeee.....eeeeeeeee.....----.eeee..eeee....eeeeeeee..........eeeeeeeeee..--------------------.eeeeeeeeeeeeeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee....ee...eeeee..------..eeeeee..........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------PILI_CHAPERONE    ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpb A   9 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEK----PFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPP--------------------DVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDL------ARNVSWRIINDQGGLDRLYSKNVT 234
                                    18        28        38        48      |  - |      68        78        88        98     |   -         -      |128       138       148       158       168       178       188       198     |   -  |    218       228      
                                                                         55   60                                         104                  125                                                                            204    211                       

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:149
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           CAF1_YERPE    22 ADLTASTTATATLVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dpbb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 3dpbB00 B:1-149  [code=2.60.40.1310, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeeee................eeeeeeee......hhh.eeee........eeeee......eeeeeeeee.....ee..ee...............eeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpb B   1 ADLTASTTVTVTVVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:131
                                    49        59        69        79        89        99       109       119       129       139       149       159       169 
           CAF1_YERPE    40 ITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dpbc_ C: automated matches                                                                                                        SCOP domains
               CATH domains 3dpbC00 C:19-149  [code=2.60.40.1310, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...ee...........eeeeeeee......hhh.eeee........eeeee......eeeeeeeee.....ee..ee.....---.......eeeeeeeeeee.......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpb C  19 ITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENL---DVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    28        38        48        58        68        78        88        98        |-  |    118       128       138       148 
                                                                                                                  107 111                                      

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DPB)

(-) Gene Ontology  (8, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAF1M_YERPE | P26926)
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).
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0043711    pilus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B,C   (CAF1_YERPE | P26948)
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).
cellular component
    GO:0042603    capsule    A protective structure surrounding some fungi and bacteria, attached externally to the cell wall and composed primarily of polysaccharides. Capsules are highly organized structures that adhere strongly to cells and cannot be easily removed. Capsules play important roles in pathogenicity, preventing phagocytosis by other cells, adherance, and resistance to dessication.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAF1M_YERPE | P269261p5u 1p5v 1z9s 2os7 3dos 3dsn 4ay0 4ayf 4az8 4b0m
        CAF1_YERPE | P269481p5u 1p5v 1z9s 3dos 3dsn 4ayf 4az8 4b0m

(-) Related Entries Specified in the PDB File

1p5u COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE ALA9ARG MUTATION IN THE GD DONOR STRAND
1z9s NATIVE CAF1M:CAF1:CAF1 COMPLEX
3dos CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE THR7PHE AND ALA9VAL MUTATIONS IN THE GD DONOR STRAND
3dsn CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE THR7PHE MUTATION IN THE GD DONOR STRAND