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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 THR7PHE AND ALA9VAL 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 :  06 Jul 08  (Deposition) - 14 Jul 09  (Release) - 14 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Beta Barrel, Protein-Protein Complex, Donor Strand Complementation, Chaperone, 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, D
    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, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 22 TO 170
    GeneCAF1, YPMT1.84, Y5196, Y1100, YP_PMT082
    MutationYES
    Organism ScientificYERSINIA PESTIS
    Organism Taxid632

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3DOS)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:98 -A:137
2D:98 -D:137

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:64 -Pro A:65
2Thr D:64 -Pro D:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.CAF1M_YERPE110-127
 
  2A:87-104
D:87-104
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.CAF1M_YERPE110-127
 
  1A:87-104
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.CAF1M_YERPE110-127
 
  1-
D:87-104

(-) Exons   (0, 0)

(no "Exon" information available for 3DOS)

(-) 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:203
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:228
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
          CAF1M_YERPE    31 ASKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 258
               SCOP domains d3dosa1 A:8-147 Chaperone protein Caf1m                                                                                                     d3dosa2 A:148-235 Caf1m                                                                  SCOP domains
               CATH domains ------3dosA01 A:14-145 PapD-like                                                                                                          ---3dosA02 A:149-232  [code=2.60.40.1070, no name defined]                             --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee...eeeee.....eeeeeee.....eeeeeeeee..-----...eeee..eeee....eeeeeeee..........eeeeeeeeee...--------------------..eeeeeeeeeeeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee....ee...eeeeee.........eeeeee..........eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dos A   8 ASKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDEN-----EDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPK--------------------VGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 235
                                    17        27        37        47    |    -|       67        77        87        97       | -         -       127       137       147       157       167       177       187       197       207       217       227        
                                                                       52    58                                            105                  126                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:148
 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 d3dosb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 3dosB00 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...............eeeeeeee.........-..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dos B   1 ADLTASFTVTATLVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLA-GKYTDAVTVTVSNQ 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   | | 140         
                                                                                                                                                               134 |             
                                                                                                                                                                 136             

Chain C from PDB  Type:PROTEIN  Length:135
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:135
                                    45        55        65        75        85        95       105       115       125       135       145       155       165     
           CAF1_YERPE    36 EPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dosc_ C: automated matches                                                                                                            SCOP domains
               CATH domains 3dosC00 C:15-149  [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
                 3dos C  15 EPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    24        34        44        54        64        74        84        94       104       114       124       134       144     

Chain D from PDB  Type:PROTEIN  Length:191
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:225
                                    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 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNV 256
               SCOP domains d3dosd1 D:9-147 Chaperone protein Caf1m                                                                                                    d3dosd2 D:148-233 Caf1m                                                                SCOP domains
               CATH domains -----3dosD01 D:14-145 PapD-like                                                                                                          ---3dosD02 D:149-232  [code=2.60.40.1070, no name defined]                             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeee.....eeeeeee.....eeeeeeee.--------..eeee..eeee....eeeeeeee..........eeeeeeeeee...-------------------.eeeeeeeeeeeeeeeeee......hhhhhhhhheeee...eeeeee.....eeeeeeee..ee....ee...eeeeee..-------.eeeee..........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------PILI_CHAPERONE    --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dos D   9 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYD--------DPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPK-------------------DVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLP-------NVSWRIINDQGGLDRLYSKNV 233
                                    18        28        38        48 |       -|       68        78        88        98      |  -         -      |128       138       148       158       168       178       188       198      |  -    |  218       228     
                                                                    50       59                                           105                 125                                                                             205     213                    

Chain E 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 d3dose_ E: automated matches                                                                                                                          SCOP domains
               CATH domains 3dosE00 E: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
                 3dos E   1 ADLTASFTVTATLVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain F from PDB  Type:PROTEIN  Length:132
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:134
                                    46        56        66        76        86        96       106       116       126       136       146       156       166    
           CAF1_YERPE    37 PARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dosf_ F: automated matches                                                                                                           SCOP domains
               CATH domains 3dosF00 F:16-149  [code=2.60.40.1310, no name defined]                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...ee...........eeeeeeee......hhh.eeeee.......eeeee......eeeeeeeee.....ee..ee....--.........eeeeeeeeeee.......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dos F  16 PARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGEN--GDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    25        35        45        55        65        75        85        95       105|  |   115       125       135       145    
                                                                                                                    106  |                                        
                                                                                                                       109                                        

   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, 8)

Asymmetric Unit

(-) CATH Domains  (3, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (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,E,F   (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 3dpb 3dsn 4ay0 4ayf 4az8 4b0m
        CAF1_YERPE | P269481p5u 1p5v 1z9s 3dpb 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
3dpb 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
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