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(-) Description

Title :  STRUCTURE OF AN RIBOSOMAL SUBUNIT INTERFACE PROTEIN FROM COXIELLA BURNETII
 
Authors :  M. Rudolph, J. Cheung, M. C. Franklin, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 28 Sep 11  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protein Synthesis, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - RIBOSOME-ASSOCIATED FACTOR Y
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBU_0745
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 777

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:13 , LYS A:55 , PRO A:57 , GLY A:58 , TYR A:71 , HOH A:119 , HOH A:130BINDING SITE FOR RESIDUE SO4 A 97
2AC2SOFTWARESER B:13 , LEU B:56 , PRO B:57 , GLY B:58 , TYR B:71 , HOH B:109BINDING SITE FOR RESIDUE SO4 B 97
3AC3SOFTWARESER C:13 , PRO C:57 , GLY C:58 , TYR C:71 , HOH C:130 , HOH C:134BINDING SITE FOR RESIDUE SO4 C 97
4AC4SOFTWARESER D:13 , LYS D:55 , PRO D:57 , GLY D:58 , TYR D:71 , HOH D:101 , HOH D:104BINDING SITE FOR RESIDUE SO4 D 97

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TQM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:28 -Pro A:29
2Gln B:28 -Pro B:29
3Gln C:28 -Pro C:29
4Gln D:28 -Pro D:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TQM)

(-) Exons   (0, 0)

(no "Exon" information available for 3TQM)

(-) 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:91
 aligned with Q83DI6_COXBU | Q83DI6 from UniProtKB/TrEMBL  Length:96

    Alignment length:91
                                    10        20        30        40        50        60        70        80        90 
          Q83DI6_COXBU    1 MHIQMTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDMYKTVDLLMHKLETQLSKYKAK 91
               SCOP domains d3tqma_ A: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhh....hhhhh.eeeeeeeee..eeeeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3tqm A  1 mHIQmTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDmYKTVDLLmHKLETQLSKYKAK 91
                            |   |   10        20        30        40        50        60        70       |80        90 
                            |   |                                                               70-MSE  78-MSE         
                            1-MSE                                                                                      
                                5-MSE                                                                                  


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with Q83DI6_COXBU | Q83DI6 from UniProtKB/TrEMBL  Length:96

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
          Q83DI6_COXBU    1 MHIQMTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDMYKTVDLLMHKLETQLSKYKAKK 92
               SCOP domains d3tqmb_ B: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhh....hhhhh.eeeeeeeee..eeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3tqm B  1 mHIQmTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDmYKTVDLLmHKLETQLSKYKAKK 92
                            |   |   10        20        30        40        50        60        70       |80        90  
                            1-MSE                                                               70-MSE  78-MSE          
                                5-MSE                                                                                   


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with Q83DI6_COXBU | Q83DI6 from UniProtKB/TrEMBL  Length:96

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
          Q83DI6_COXBU    1 MHIQMTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDMYKTVDLLMHKLETQLSKYKAKKG 93
               SCOP domains d3tqmc_ C: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhh....hhhhh.eeeeeeeee..eeeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3tqm C  1 mHIQmTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDmYKTVDLLmHKLETQLSKYKAKKG 93
                            |   |   10        20        30        40        50        60        70       |80        90   
                            1-MSE                                                               70-MSE  78-MSE           
                                5-MSE                                                                                    


Chain D from PDB  Type:PROTEIN  Length:93
 aligned with Q83DI6_COXBU | Q83DI6 from UniProtKB/TrEMBL  Length:96

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
          Q83DI6_COXBU    1 MHIQMTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDMYKTVDLLMHKLETQLSKYKAKKG 93
               SCOP domains d3tqmd_ D: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhh....hhhhh.eeeeeeeee..eeeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3tqm D  1 mHIQmTGQGVDISPALRELTEKKLHRIQPCRDEISNIHIIFHINKLKKIVDANVKLPGSTINAQAESDDmYKTVDLLmHKLETQLSKYKAKKG 93
                            |   |   10        20        30        40        50        60        70       |80        90   
                            1-MSE                                                               70-MSE  78-MSE           
                                5-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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TQM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q83DI6_COXBU | Q83DI6)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0044238    primary metabolic process    The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.

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