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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN-UBIQUITIN FUSION PROTEIN
 
Authors :  N. Suzuki, S. Wakatsuki, M. Kawasaki
Date :  10 May 10  (Deposition) - 29 Sep 10  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Green Fluorescent Protein, Ubiquitin, Fusion Protein, Fluorescent Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Suzuki, M. Hiraki, Y. Yamada, N. Matsugaki, N. Igarashi, R. Kato, I. Dikic, D. Drew, S. Iwata, S. Wakatsuki, M. Kawasaki
Crystallization Of Small Proteins Assisted By Green Fluorescent Protein
Acta Crystallogr. , Sect. D V. 66 1059 2010
PubMed-ID: 20944239  |  Reference-DOI: 10.1107/S0907444910032944

(-) Compounds

Molecule 1 - YEAST ENHANCED GREEN FLUORESCENT PROTEIN,UBIQUITIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-230 FOR YEAST ENHANCED GREEN FLUORESCENT PROTEIN,RESIDUES 1-74 FOR UBIQUITIN
    Organism Common: JELLYFISH, MOUSE
    Organism Scientific: AEQUOREA VICTORIA, MUS MUSCULUS
    Organism Taxid: 6100, 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CR21Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:142 , TYR A:143 , SER A:202 , HOH A:378 , HOH A:607BINDING SITE FOR RESIDUE EDO A 315
2AC2SOFTWAREGLU A:34 , ASP A:36 , LYS A:41 , THR A:43 , HOH A:449 , HOH A:465BINDING SITE FOR RESIDUE EDO A 316
3AC3SOFTWAREARG A:96 , THR A:97 , GLY A:116 , ASP A:117 , TYR A:182 , EDO A:319 , HOH A:553BINDING SITE FOR RESIDUE EDO A 317
4AC4SOFTWAREARG A:109 , GLU A:111 , ARG A:122 , GLU A:124BINDING SITE FOR RESIDUE EDO A 318
5AC5SOFTWAREGLU A:95 , ARG A:96 , THR A:108 , EDO A:317 , HOH A:506BINDING SITE FOR RESIDUE EDO A 319

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AI5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AI5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AI5)

(-) Exons   (0, 0)

(no "Exon" information available for 3AI5)

(-) 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:300
 aligned with E9Q9J0_MOUSE | E9Q9J0 from UniProtKB/TrEMBL  Length:96

    Alignment length:300
                                                                                                                                                                                                                                                                 1                                                                      
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71
         E9Q9J0_MOUSE     - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL  71
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.....eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ai5 A   2 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFgVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 303
                                    11        21        31        41        51        61  |||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303
                                                                                         64||                                                                                                                                                                                                                                           
                                                                                          66-CR2                                                                                                                                                                                                                                        
                                                                                           68
   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  (0, 0)

(no "SCOP Domain" information available for 3AI5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AI5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AI5)

(-) Gene Ontology  (41, 72)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E9Q9J0_MOUSE | E9Q9J0)
molecular function
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    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.

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    Met A:88 - Pro A:89   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL40_MOUSE | P62984: 1cmx 1gjz 1ud7 1uzx 2znv 3a1q 3a9j 3a9k
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        E9Q9J0_MOUSE | E9Q9J0: 3vht

(-) Related Entries Specified in the PDB File

3ai4 CRYSTAL STRUCTURE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN - MOUSE POLYMERASE IOTA UBIQUITIN BINDING MOTIF FUSION PROTEIN