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(-) Description

Title :  CRYSTAL STRUCTURE OF ERA IN COMPLEX WITH GDP
 
Authors :  C. Tu, X. Ji
Date :  23 Jul 09  (Deposition) - 25 Aug 09  (Release) - 13 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Era, Gtpase, Kh Domain, Gdp, Cell Membrane, Gtp-Binding, Membrane, Nucleotide-Binding, Phosphoprotein, Rna-Binding, Nucleotide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tu, X. Zhou, J. E. Tropea, B. P. Austin, D. S. Waugh, D. L. Court, X. Ji
Structure Of Era In Complex With The 3' End Of 16S Rrna: Implications For Ribosome Biogenesis
Proc. Natl. Acad. Sci. Usa V. 106 14843 2009
PubMed-ID: 19706445  |  Reference-DOI: 10.1073/PNAS.0904032106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN ERA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE31
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2566, ERA, ESCHERICHIA COLI, JW2550, RBAA
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: GENOMIC DNA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2SO413Ligand/IonSULFATE ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2SO45Ligand/IonSULFATE ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2SO48Ligand/IonSULFATE ION
3TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:18 , VAL A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , ASN A:124 , LYS A:125 , ASP A:127 , SER A:155 , ALA A:156 , GLU A:157BINDING SITE FOR RESIDUE GDP A 302
02AC2SOFTWAREASN B:18 , VAL B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , ASN B:124 , LYS B:125 , ASP B:127 , SER B:155 , ALA B:156 , GLU B:157 , HOH B:320BINDING SITE FOR RESIDUE GDP B 302
03AC3SOFTWARETRP A:285 , ARG A:293BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREARG A:46 , THR A:63 , PRO A:64BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREARG A:113 , ASN A:147BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWARETRP B:285 , ARG B:293BINDING SITE FOR RESIDUE SO4 B 303
07AC7SOFTWAREARG B:46 , THR B:63BINDING SITE FOR RESIDUE SO4 B 304
08AC8SOFTWARESER B:189 , GLN B:190 , ARG B:191 , HOH B:326BINDING SITE FOR RESIDUE SO4 B 305
09AC9SOFTWARELYS B:280 , GLY B:284 , TRP B:285 , ARG B:290BINDING SITE FOR RESIDUE SO4 B 307
10BC1SOFTWARELYS A:280 , GLY A:284 , TRP A:285 , ARG A:290BINDING SITE FOR RESIDUE SO4 A 306
11BC2SOFTWAREARG A:191 , GLU A:219 , ARG A:220 , PHE A:221BINDING SITE FOR RESIDUE SO4 A 307
12BC3SOFTWAREGLU B:69 , ARG B:72 , ARG B:76BINDING SITE FOR RESIDUE SO4 B 308
13BC4SOFTWARETHR B:99 , ARG B:100 , ASN B:128 , GLN B:130BINDING SITE FOR RESIDUE SO4 B 309
14BC5SOFTWAREARG B:44BINDING SITE FOR RESIDUE SO4 B 310
15BC6SOFTWARELYS A:27 , GLY A:30 , HIS A:51 , GLU A:53 , HOH A:322BINDING SITE FOR RESIDUE TRS A 308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IEU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_ERAPS51713 Era-type guanine nucleotide-binding (G) domain profile.ERA_ECOLI7-175
 		  2A:7-175
B:7-175
2KH_TYPE_2PS50823 Type-2 KH domain profile.ERA_ECOLI206-283
 		  2A:206-283
B:206-283
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_ERAPS51713 Era-type guanine nucleotide-binding (G) domain profile.ERA_ECOLI7-175
 		  1A:7-175
-
2KH_TYPE_2PS50823 Type-2 KH domain profile.ERA_ECOLI206-283
 		  1A:206-283
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_ERAPS51713 Era-type guanine nucleotide-binding (G) domain profile.ERA_ECOLI7-175
 		  1-
B:7-175
2KH_TYPE_2PS50823 Type-2 KH domain profile.ERA_ECOLI206-283
 		  1-
B:206-283

(-) Exons   (0, 0)

(no "Exon" information available for 3IEU)

(-) 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:293
 aligned with ERA_ECOLI | P06616 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
            ERA_ECOLI     4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSLG 296
               SCOP domains d3ieua1 A:4-182 GTPase Era, N-terminal domain                                                                                                                                      d3ieua2 A:183-296 GTPase Era C-terminal domain                                                                     SCOP domains
               CATH domains 3ieuA01 A:4-184 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh..eeee..........eeeeeee..eeeeee.....hhhhhhhhhhhhh.........eeeeeeeee....hhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.....eeee.......hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---G_ERA  PDB: A:7-175 UniProt: 7-175                                                                                                                                       ------------------------------KH_TYPE_2  PDB: A:206-283 UniProt: 206-283                                    ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieu A   4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSLG 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with ERA_ECOLI | P06616 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
            ERA_ECOLI     4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSLG 296
               SCOP domains d3ieub1 B:4-182 GTPase Era, N-terminal domain                                                                                                                                      d3ieub2 B:183-296 GTPase Era C-terminal domain                                                                     SCOP domains
               CATH domains 3ieuB01 B:4-184 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh..eeee..........eeeeeee..eeeeee.....hhhhhhhhhhhhh.........eeeeeeeee....hhhhhhhhhhhhh....eeeeeehhhhh....hhhhhhhhhhh.....eeee.......hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---G_ERA  PDB: B:7-175 UniProt: 7-175                                                                                                                                       ------------------------------KH_TYPE_2  PDB: B:206-283 UniProt: 206-283                                    ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieu B   4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSLG 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ERA_ECOLI | P06616)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0070181    small ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA.
biological process
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042274    ribosomal small subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ERA_ECOLI | P06616: 1ega 1x1l

(-) Related Entries Specified in the PDB File

1ega LIGAND-FREE E. COLI ERA
1wf3 T. THERMOPHILUS ERA IN COMPLEX WITH MGGNP
1x1l CRYO-EM MODEL OF ERA IN COMPLEX WITH THE 3' MINOR DOMAIN OF 16S RRNA WITHIN THE MATURE 30S RIBOSOME