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(-) Description

Title :  STRUCTURE DETERMINATION BY MAD: E.COLI TRIGGER FACTOR BINDING AT THE RIBOSOMAL EXIT TUNNEL.
 
Authors :  O. Kristensen, M. Gajhede
Date :  26 Feb 03  (Deposition) - 16 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alpha-Beta Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kristensen, M. Gajhede
Chaperone Binding At The Ribosomal Exit Tunnel.
Structure V. 11 1547 2003
PubMed-ID: 14656439  |  Reference-DOI: 10.1016/J.STR.2003.11.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIGGER FACTOR
    Chains: A, B, C
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RIBOSOME BINDING DOMAIN
    Gene: TIG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric/Biological Unit (5, 29)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE9Mod. Amino AcidSELENOMETHIONINE
3PG45Ligand/IonTETRAETHYLENE GLYCOL
4SO21Ligand/IonSULFUR DIOXIDE
5SO413Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:42 , GLY A:43 , ARG A:45 , GLU B:114 , HOH B:627BINDING SITE FOR RESIDUE SO4 B 501
02AC2SOFTWAREARG A:57 , LYS C:98 , LEU C:99 , SO4 C:508 , HOH C:533BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREARG B:40 , LYS B:46 , HOH B:639 , HOH B:644BINDING SITE FOR RESIDUE SO4 B 503
04AC4SOFTWAREARG B:40 , ILE B:41 , ASP B:42 , GLY B:43 , ARG B:45 , LYS B:48 , HOH B:628 , HOH B:659BINDING SITE FOR RESIDUE SO4 B 504
05AC5SOFTWAREPRO A:50 , MSE A:51 , HOH A:535 , LYS C:29 , ARG C:40 , ARG C:45BINDING SITE FOR RESIDUE SO4 C 505
06AC6SOFTWARELYS A:37 , THR B:8 , ARG B:14BINDING SITE FOR RESIDUE SO4 C 506
07AC7SOFTWAREGLN C:9 , GLY C:10 , ARG C:13 , HOH C:521 , HOH C:585BINDING SITE FOR RESIDUE SO4 C 507
08AC8SOFTWAREARG A:45 , ARG A:57 , SO4 A:502 , SO4 A:514 , ASN B:85 , TYR B:112 , HOH B:614BINDING SITE FOR RESIDUE SO4 C 508
09AC9SOFTWAREPHE B:44 , ARG B:45 , HOH B:637 , HOH B:656BINDING SITE FOR RESIDUE SO4 B 509
10BC1SOFTWARELYS A:98 , LEU A:99 , HOH A:548 , HOH A:560 , ARG C:57 , ASN C:85BINDING SITE FOR RESIDUE SO4 A 510
11BC2SOFTWARELYS B:29 , PRO B:50 , MSE B:51BINDING SITE FOR RESIDUE SO4 B 511
12BC3SOFTWAREGLY A:47 , LYS A:48 , GLN B:9 , GLY B:10 , ASP C:42BINDING SITE FOR RESIDUE SO4 A 512
13BC4SOFTWAREGLN A:56 , ARG A:57 , TYR B:112 , HOH B:615 , PG4 C:402 , SO4 C:508BINDING SITE FOR RESIDUE SO4 A 514
14BC5SOFTWAREGLY A:68 , GLN B:64 , GLY B:95 , PG4 B:404BINDING SITE FOR RESIDUE PG4 B 401
15BC6SOFTWARESO4 A:514 , TYR B:112 , PRO B:113 , ALA C:60 , ALA C:89 , HOH C:515 , HOH C:518 , HOH C:553BINDING SITE FOR RESIDUE PG4 C 402
16BC7SOFTWAREGLN C:64 , MSE C:71 , SER C:72 , TYR C:92 , HOH C:543 , HOH C:578BINDING SITE FOR RESIDUE PG4 C 403
17BC8SOFTWAREGLN A:64 , ASP A:65 , MSE B:71 , SER B:72 , TYR B:92 , PG4 B:401 , HOH B:610BINDING SITE FOR RESIDUE PG4 B 404
18BC9SOFTWAREVAL C:93 , PRO C:94 , GLY C:95 , SER C:106BINDING SITE FOR RESIDUE PG4 C 405
19CC1SOFTWAREARG B:40 , ARG B:45 , LYS B:46BINDING SITE FOR RESIDUE SO2 B 601
20CC2SOFTWARELYS A:29 , MSE C:51 , ASN C:52 , HOH C:544 , HOH C:558BINDING SITE FOR RESIDUE GOL C 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OMS)

(-) 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:115
 aligned with TIG_ECOLI | P0A850 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
            TIG_ECOLI     1 MQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPMNIVAQRYGASVRQDVLGDLMSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEV 115
               SCOP domains d1omsa_ A: Trigger factor ribosome-binding domain                                                                   SCOP domains
               CATH domains -1omsA00 A:2-115 Trigger factor ribosome binding domain; domain 1                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee........eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1oms A   1 mQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPmNIVAQRYGASVRQDVLGDLmSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEV 115
                            |       10        20        30        40        50|       60        70|       80        90       100       110     
                            |                                                51-MSE              71-MSE                                        
                            1-MSE                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with TIG_ECOLI | P0A850 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
            TIG_ECOLI     1 MQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPMNIVAQRYGASVRQDVLGDLMSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVE 116
               SCOP domains d1omsb_ B: Trigger factor ribosome-binding domain                                                                    SCOP domains
               CATH domains -1omsB00 B:2-116 Trigger factor ribosome binding domain; domain 1                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee........eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oms B   1 mQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPmNIVAQRYGASVRQDVLGDLmSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVE 116
                            |       10        20        30        40        50|       60        70|       80        90       100       110      
                            1-MSE                                            51-MSE              71-MSE                                         


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with TIG_ECOLI | P0A850 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:118
                             1                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109        
            TIG_ECOLI     - -MQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPMNIVAQRYGASVRQDVLGDLMSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVEL 117
               SCOP domains d1omsc_ C: Trigger factor ribosome-binding domain                                                                      SCOP domains
               CATH domains 1omsC00 C:0-117 Trigger factor ribosome binding domain; domain 1                                                       CATH domains
           Pfam domains (1) -Trigger_N-1omsC01 C:1-117                                                                                             Pfam domains (1)
           Pfam domains (2) -Trigger_N-1omsC02 C:1-117                                                                                             Pfam domains (2)
           Pfam domains (3) -Trigger_N-1omsC03 C:1-117                                                                                             Pfam domains (3)
         Sec.struct. author ...eeeee....eeeeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1oms C   0 HmQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPmNIVAQRYGASVRQDVLGDLmSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVEL 117
                             |       9        19        29        39        49 |      59        69 |      79        89        99       109        
                             1-MSE                                            51-MSE              71-MSE
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Trigger_N] (4)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (TIG_ECOLI | P0A850)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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:0044183    protein binding involved in protein folding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    GO:0051083    'de novo' cotranslational protein folding    The process of assisting in the correct noncovalent assembly of the ribosome-bound nascent chains of a multidomain protein whilst other parts of the protein are still being translated.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    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:0043335    protein unfolding    The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
    GO:0009408    response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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        TIG_ECOLI | P0A850: 1l1p 1p9y 1w26 1w2b 2mlx 2mly 2mlz 2vrh 4urd

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