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(-) Description

Title :  VERSATILE MODES OF PEPTIDE RECOGNITION BY THE AAA+ ADAPTOR PROTEIN SSPB- THE CRYSTAL STRUCTURE OF A SSPB-RSEA COMPLEX
 
Authors :  I. Levchenko, R. A. Grant, J. M. Flynn, R. T. Sauer, T. A. Baker
Date :  03 Jan 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Protein-Peptide Complex, Sspb, Rsea, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Levchenko, R. A. Grant, J. M. Flynn, R. T. Sauer, T. A. Baker
Versatile Modes Of Peptide Recognition By The Aaa+ Adaptor Protein Sspb
Nat. Struct. Mol. Biol. V. 12 520 2005
PubMed-ID: 15880122  |  Reference-DOI: 10.1038/NSMB934
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STRINGENT STARVATION PROTEIN B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SSPB PEPTIDE-BINDING DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - SIGMA-E FACTOR NEGATIVE REGULATORY PROTEIN
    Chains: E, F, G, H
    Engineered: YES
    Fragment: RSEA N-TERMINAL FRAGMENT
    Other Details: THIS SEQUENCE CORRESPONDS TO RESIDUES 77 - 108 OF E. COLI PROTEIN RSEA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YFN)

(-) Sites  (0, 0)

(no "Site" information available for 1YFN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YFN)

(-) Exons   (0, 0)

(no "Exon" information available for 1YFN)

(-) 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:109
 aligned with SSPB_ECOLI | P0AFZ3 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:109
                                    12        22        32        42        52        62        72        82        92       102         
           SSPB_ECOLI     3 LSQLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
               SCOP domains d1yfna_ A: automated matches                                                                                  SCOP domains
               CATH domains 1yfnA00 A:3-111 Stringent starvation protein B, SspB                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh...eeeeee........hhhhh...eeeee.hhhhheeeee...eeeeeeee..eeeeeeee...eeeeee.....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1yfn A   3 LSQLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
                                    12        22        32        42        52        62        72        82        92       102         


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with SSPB_ECOLI | P0AFZ3 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           SSPB_ECOLI     5 QLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
               SCOP domains d1yfnb_ B: automated matches                                                                                SCOP domains
               CATH domains 1yfnB00 B:5-111 Stringent starvation protein B, SspB                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh....eeeeee........hhhhh...eeeee.hhhhheeeee...eeeeeeee..eeeeeeee...eeeeee.....eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1yfn B   5 QLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
                                    14        24        34        44        54        64        74        84        94       104       


Chain C from PDB  Type:PROTEIN  Length:107
 aligned with SSPB_ECOLI | P0AFZ3 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           SSPB_ECOLI     5 QLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
               SCOP domains d1yfnc_ C: automated matches                                                                                SCOP domains
               CATH domains 1yfnC00 C:5-111 Stringent starvation protein B, SspB                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh....eeeeee........hhhhh...eeeee.hhhhheeeee...eeeeeeee..eeeeeeee...eeeeee.....eee...hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1yfn C   5 QLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
                                    14        24        34        44        54        64        74        84        94       104       


Chain D from PDB  Type:PROTEIN  Length:107
 aligned with SSPB_ECOLI | P0AFZ3 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
           SSPB_ECOLI     5 QLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
               SCOP domains d1yfnd_ D: automated matches                                                                                SCOP domains
               CATH domains 1yfnD00 D:5-111 Stringent starvation protein B, SspB                                                        CATH domains
           Pfam domains (1) SspB-1yfnD01 D:5-111                                                                                        Pfam domains (1)
           Pfam domains (2) SspB-1yfnD02 D:5-111                                                                                        Pfam domains (2)
           Pfam domains (3) SspB-1yfnD03 D:5-111                                                                                        Pfam domains (3)
           Pfam domains (4) SspB-1yfnD04 D:5-111                                                                                        Pfam domains (4)
         Sec.struct. author ....hhhhhhhhhhhhhhhh...eeeeee........hhhhh...eeeee.hhhhheeeee...eeeeeeee..eeeeeeee...eeeeee.....eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1yfn D   5 QLTPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVQVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGIPRQVSVPLAAVLAIYARENGAGTMFEPEAAYD 111
                                    14        24        34        44        54        64        74        84        94       104       


Chain E from PDB  Type:PROTEIN  Length:18
 aligned with RSEA_ECOL6 | P0AFX8 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:18
                                    86        
           RSEA_ECOL6    77 EAQPAPHQWQKMPFWQKV  94
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 1yfn E   1 EAQPAPHQWQKMPFWQKV  18
                                    10        


Chain E from PDB  Type:PROTEIN  Length:18
 aligned with RSEA_ECOLI | P0AFX7 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:18
                                    86        
           RSEA_ECOLI    77 EAQPAPHQWQKMPFWQKV  94
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 1yfn E   1 EAQPAPHQWQKMPFWQKV  18
                                    10        


Chain F from PDB  Type:PROTEIN  Length:15
 aligned with RSEA_ECOL6 | P0AFX8 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:15
                                    86     
           RSEA_ECOL6    77 EAQPAPHQWQKMPFW  91
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1yfn F   1 EAQPAPHQWQKMPFW  15
                                    10     


Chain F from PDB  Type:PROTEIN  Length:15
 aligned with RSEA_ECOLI | P0AFX7 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:15
                                    86     
           RSEA_ECOLI    77 EAQPAPHQWQKMPFW  91
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1yfn F   1 EAQPAPHQWQKMPFW  15
                                    10     


Chain G from PDB  Type:PROTEIN  Length:15
 aligned with RSEA_ECOL6 | P0AFX8 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:15
                                    86     
           RSEA_ECOL6    77 EAQPAPHQWQKMPFW  91
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1yfn G   1 EAQPAPHQWQKMPFW  15
                                    10     


Chain G from PDB  Type:PROTEIN  Length:15
 aligned with RSEA_ECOLI | P0AFX7 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:15
                                    86     
           RSEA_ECOLI    77 EAQPAPHQWQKMPFW  91
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1yfn G   1 EAQPAPHQWQKMPFW  15
                                    10     


Chain H from PDB  Type:PROTEIN  Length:15
 aligned with RSEA_ECOL6 | P0AFX8 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:15
                                    86     
           RSEA_ECOL6    77 EAQPAPHQWQKMPFW  91
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
           Pfam domains (1) RseA_N-1yfnH0-- Pfam domains (1)
           Pfam domains (2) RseA_N-1yfnH0-- Pfam domains (2)
           Pfam domains (3) RseA_N-1yfnH0-- Pfam domains (3)
           Pfam domains (4) RseA_N-1yfnH0-- Pfam domains (4)
         Sec.struct. author ....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1yfn H   1 EAQPAPHQWQKMPFW  15
                                    10     


Chain H from PDB  Type:PROTEIN  Length:15
 aligned with RSEA_ECOLI | P0AFX7 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:15
                                    86     
           RSEA_ECOLI    77 EAQPAPHQWQKMPFW  91
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
           Pfam domains (1) RseA_N-1yfnH0-- Pfam domains (1)
           Pfam domains (2) RseA_N-1yfnH0-- Pfam domains (2)
           Pfam domains (3) RseA_N-1yfnH0-- Pfam domains (3)
           Pfam domains (4) RseA_N-1yfnH0-- Pfam domains (4)
         Sec.struct. author ....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 1yfn H   1 EAQPAPHQWQKMPFW  15
                                    10
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: RseA_N] (2)
(-)
Clan: no clan defined [family: SspB] (10)

(-) Gene Ontology  (12, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SSPB_ECOLI | P0AFZ3)
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:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain E,F,G,H   (RSEA_ECOL6 | P0AFX8)
molecular function
    GO:0016989    sigma factor antagonist activity    The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
biological process
    GO:1903506    regulation of nucleic acid-templated transcription    Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
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.

Chain E,F,G,H   (RSEA_ECOLI | P0AFX7)
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).
    GO:0016989    sigma factor antagonist activity    The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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.

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  1yfn
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  RSEA_ECOLI | P0AFX7
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  SSPB_ECOLI | P0AFZ3
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 Related Entries

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

UniProtKB/Swiss-Prot
        RSEA_ECOLI | P0AFX7: 1or7 3m4w
        SSPB_ECOLI | P0AFZ3: 1ox8 1ox9 2ds8

(-) Related Entries Specified in the PDB File

1ou8 1ou9 1oul 1ox8 1ox9