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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE CRYSTAL STRUCTURE OF UNCHARACTERIZED PROTEIN LOC79017 FROM HOMO SAPIENS
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  31 May 07  (Deposition) - 19 Jun 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B  (4x)
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Bae, C. A. Bingman, D. J. Aceti, G. N. Phillips Jr.
Crystal Structure Of Homo Sapiens Protein Loc79017.
Proteins V. 70 588 2008
PubMed-ID: 17932939  |  Reference-DOI: 10.1002/PROT.21719
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN C7ORF24
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVP30
    Expression System StrainBL834(DE3) PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneC7ORF24
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (4x)AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2Q53)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q53)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q53)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q53)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q53)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002754281aENSE00001181767chr7:30544460-30544185276GGCT_HUMAN1-47472A:14-47
B:15-47
34
33
1.2aENST000002754282aENSE00000674843chr7:30540297-30540152146GGCT_HUMAN48-96492A:48-96
B:48-96
49
49
1.4cENST000002754284cENSE00001674226chr7:30538554-30538419136GGCT_HUMAN96-141462A:96-141
B:96-141
46
46
1.6fENST000002754286fENSE00001909539chr7:30536851-30536237615GGCT_HUMAN142-188472A:142-182
B:142-183
41
42

(-) 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:169
 aligned with GGCT_HUMAN | O75223 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:169
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173         
           GGCT_HUMAN    14 EESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGNSQGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQEGVKSGMYVVIEVKVATQEGKEITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSEEIEDIIKK 182
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2q53A00 A:14-182 Hypothetical upf0131 protein ytfp                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhh...eeeeeeeeeeeeeeeeee...........eeeeeeeeeeeeeeeeeeee..hhhhhhhhh.......eeeeeeee.....eeeeeeee...eee...hhhhhhhhhhhhhhh..hhhhhhhhhh..........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:14-47           Exon 1.2a  PDB: A:48-96 UniProt: 48-96           ---------------------------------------------Exon 1.6f  PDB: A:142-182 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.4c  PDB: A:96-141 UniProt: 96-141      ----------------------------------------- Transcript 1 (2)
                 2q53 A  14 EESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGNSQGKTSQTWHGGIATIFQSPGDEVWGVVWKmNKSNLNSLDEQEGVKSGmYVVIEVKVATQEGKEITCRSYLmTNYESAPPSPQYKKIICmGAKENGLPLEYQEKLKAIEPNDYTGKVSEEIEDIIKK 182
                                    23        33        43        53        63        73        83  |     93       103|      113       123   |   133       143 |     153       163       173         
                                                                                                   86-MSE           104-MSE                127-MSE           145-MSE                                 

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with GGCT_HUMAN | O75223 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:169
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174         
           GGCT_HUMAN    15 ESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGNSQGKTSQTWHGGIATIFQSPGDEVWGVVWKMNKSNLNSLDEQEGVKSGMYVVIEVKVATQEGKEITCRSYLMTNYESAPPSPQYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGKVSEEIEDIIKKG 183
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2q53B00 B:15-183 Hypothetical upf0131 protein ytfp                                                                                                                        CATH domains
           Pfam domains (1) ---------------------------------------------------------------AIG2_2-2q53B01 B:78-160                                                            ----------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------AIG2_2-2q53B02 B:78-160                                                            ----------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.hhhhhhhhhh......eeeeeeeeeeeeeeeeee...........eeeeeeeeeeeeeeeeeeee..hhhhhhhhh.......eeeeeeee.....eeeeeeee...eee...hhhhhhhhhhhhhhh..hhhhhhhhhhh.........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:15-47          Exon 1.2a  PDB: B:48-96 UniProt: 48-96           ---------------------------------------------Exon 1.6f  PDB: B:142-183 UniProt: 142-188 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------Exon 1.4c  PDB: B:96-141 UniProt: 96-141      ------------------------------------------ Transcript 1 (2)
                 2q53 B  15 ESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGNSQGKTSQTWHGGIATIFQSPGDEVWGVVWKmNKSNLNSLDEQEGVKSGmYVVIEVKVATQEGKEITCRSYLmTNYESAPPSPQYKKIICmGAKENGLPLEYQEKLKAIEPNDYTGKVSEEIEDIIKKG 183
                                    24        34        44        54        64        74        84 |      94       104       114       124  |    134       144|      154       164       174         
                                                                                                  86-MSE           104-MSE                127-MSE           145-MSE                                  

   Legend:   → Mismatch (orange background)
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  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 2Q53)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AIG2 (6)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GGCT_HUMAN | O75223)
molecular function
    GO:0003839    gamma-glutamylcyclotransferase activity    Catalysis of the reaction: (5-L-glutamyl)-L-amino acid = 5-oxoproline + L-amino acid.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
    GO:0001836    release of cytochrome c from mitochondria    The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GGCT_HUMAN | O752232i5t 2pn7 2rbh 3cry

(-) Related Entries Specified in the PDB File

2i5t ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.