PDBsum entry 3by7

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protein Protein-protein interface(s) links
Unknown function PDB id
Protein chains
80 a.a.
82 a.a.
86 a.a.
76 a.a.
Waters ×7
PDB id:
Name: Unknown function
Title: Crystal structure of a protein structurally similar to sm/ls RNA-binding proteins (jcvi_pep_1096686650277) from uncultur organism at 2.60 a resolution
Structure: Uncharacterized protein. Chain: a, b, c, d, e. Engineered: yes
Source: Uncultured marine organism. Organism_taxid: 360281. Gene: synthetic gene: the gene product was based on jcvi_pep_1096686650277 from the sorcerer ii global ocean sa experiment. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.60Å     R-factor:   0.238     R-free:   0.285
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
D.Das et al. (2009). Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution. Proteins, 75, 296-307. PubMed id: 19173316 DOI: 10.1002/prot.22360
15-Jan-08     Release date:   29-Jan-08    
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Protein chains
No UniProt id for this chain
Struc: 80 a.a.
Protein chain
No UniProt id for this chain
Struc: 82 a.a.
Protein chain
No UniProt id for this chain
Struc: 86 a.a.
Protein chain
No UniProt id for this chain
Struc: 76 a.a.
Key:    Secondary structure  CATH domain


DOI no: 10.1002/prot.22360 Proteins 75:296-307 (2009)
PubMed id: 19173316  
Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.
D.Das, P.Kozbial, H.L.Axelrod, M.D.Miller, D.McMullan, S.S.Krishna, P.Abdubek, C.Acosta, T.Astakhova, P.Burra, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, Y.Elias, M.A.Elsliger, D.Ernst, C.Farr, J.Feuerhelm, A.Grzechnik, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, A.T.Morse, K.D.Murphy, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, S.Sudek, H.Tien, C.Trame, C.V.Trout, H.van den Bedem, D.Weekes, A.White, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.
  Selected figure(s)  
Figure 3.
Figure 3. (A) Residues conserved among the ECX21941 homologs are depicted in the schematic view of the pentamer by a black ball-and-stick representation. Each monomer is highlighted in a different color. For clarity, conserved residues are labeled on one monomer only. (B) The electrostatic surface potential of the pentamer formed by ECX21941 (top and bottom view) shows a ring of positively charged amino acids in blue (n.b. negatively charged amino acids are in red and neutral in white) on the outer periphery and a region of charged residues lining the entrance to the central pore. Lys67 constitutes the positively charged region at the entrance to the pore from the top side lining the central pore. Going from top to bottom, a negatively charged region is formed from Asp64, Asp65, and Ser66 prior to Lys67. The positively charged patch on the outer periphery of the top surface arises from Lys2, Lys5, Lys29, Lys30, Lys59, and Lys75.
Figure 4.
Figure 4. (A) Clusters of ECX21941 homologs from marine metagenome-specific dataset of Sm-like proteins. Lines represent BLAST hits with P-value 5e^-39. (B) The same as above, but the BLAST hits with P-value 5e^-9 are shown. (C) Multiple sequence alignment of ECX21941 and its homologs from marine metagenome dataset. Prochlorococcus cyanophage P-SSM2 (YP_214412, YP_214375, and YP_214413), Synechococcus cyanophage syn9 (YP_717827, YP_717841, and YP_717812), Synechococcus cyanophage S-PM2 (YP_195166, YP_195147, and YP_195167), Prochlorococcus cyanophage P-SSM4 (YP_214705 and YP_214678), and Synechococcus sp. RS9916 (ZP_01472537). Numbers in parentheses indicate number of residues omitted for clarity. The conservation scores [ranging from 0 (not conserved) to 4 (highly conserved); 4 with bold and underlined font, the most conserved] for all homologs and for the most abundant clusters (A-F) were derived from an analysis using rate4site software using all available homologs of ECX21941 and not just those shown in the alignment. Residues are highlighted according to the amino acid properties. Red shading indicates conservation of single residue. Brown font with yellow shading indicates conservation of aliphatic residues (I, L, V). Green font indicates conservation of the smallest residues (A, G, and S). Blue font with yellow shading indicates conservation of aromatic residues (F, H, W, and Y). Dark green font indicates conservation of small residues (A, C, D, G, N, P, S, T, and V). Red font indicates conservation of polar residues (C, D, E, H, K, N, Q, R, S, and T). Blue font with green shading indicates conservation of large residues (E, F, H, I, K, L, M, Q, R, W, and Y). Black font with yellow shading indicates conservation of hydrophobic residues (A, C, F, G, H, I, L, M, T, V, W, and Y).
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 75, 296-307) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20429930 A.Prlić, M.A.Martinez, D.Dimitropoulos, B.Beran, B.T.Yukich, P.W.Rose, P.E.Bourne, and J.L.Fink (2010).
Integration of open access literature into the RCSB Protein Data Bank using BioLit.
  BMC Bioinformatics, 11, 220.  
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