Protein Structure

The so-called MIF4G domain found in several other proteins involved in RNA metabolism. (Mazza et al.)(PDB no: 1H6K)

- Coordinates assembly of translational machinery

DALI results

1. 1. SUMMARY: PDB/chain identifiers and structural alignment statistics

 NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
  1: 3028-A 2i2o-A 37.1  0.0  206   206  100      0      0     1 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	eif4g-like prote
  2: 3028-A 1hu3-A 15.2  2.7  164   204   23      0      0    12 S     TRANSLATION 	eif4gii fragment (eukaryotic initiation f
  3: 3028-A 1uw4-B 10.9  3.6  164   247    9      0      0    12 S    NONSENSE MEDIATED MRNA DECAY PROTEIN 	regulator of nons
  4: 3028-A 1h6k-A 10.6  3.9  175   728   11      0      0    11 S     NUCLEAR PROTEIN 	cbp80 fragment (ncbp 80 kda subunit, 
  5: 3028-A 2db0-A  8.1  3.3  148   239   14      0      0    13 S    PROTEIN BINDING 	253aa long hypothetical protein (hypot
  6: 3028-A 1b3u-A  8.0 27.7  150   588   13      0      0    13 S    SCAFFOLD PROTEIN 	protein phosphatase pp2a fragment

ClustalW Results

Using the scores and results from DALI, a multiple sequence alignment was created with ClustalW. The sequences used were:

• 2i2o Structural Genomics, unknown function
• 1hu3 Translation eif4gii fragment
• 1uw4 nonsense mediated mRNA decay protein
• 1h6k Nuclear Protein

(refer to DALI table if unsure)

Generally, the alignment shows PATHETIC HOMOLOGY between these 4 sequences, which were already the best sequences that DALI could give. To view results, click here [1]

3D structural results using SSM (Analysis 1)

Not too sure what the results mean. to view results, click here [2]

The sequences used were:

• 2i2o Structural Genomics, unknown function
• 1hu3 Translation eif4gii fragment
• 1uw4 nonsense mediated mRNA decay protein
• 1h6k Nuclear Protein

(refer to DALI table if unsure)

3D structural results using SSM (Analysis 2)

There is a slight difference compared to the resu;ts above. The sequences used in this analysis are different from the one above. To view results, click here [3]

The sequences used were:

• 2i2o Structural Genomics, unknown function
• 1hu3 Translation eif4gii fragment
• 1uw4 nonsense mediated mRNA decay protein
• 2db0 hypothetical Protein

(refer to DALI table if unsure)

Scorecons results (Analysis 1)

Gives a score to the conserved residue of the msa. The sequences used were:

• 2i2o Structural Genomics, unknown function
• 1hu3 Translation eif4gii fragment
• 1uw4 nonsense mediated mRNA decay protein
• 1h6k Nuclear Protein

To view results, click here [4]

Scorecons results (Analysis 2)

Gives a score to the conserved residue of the msa. The sequences used were:

• 2i2o Structural Genomics, unknown function
• 1hu3 Translation eif4gii fragment
• 1uw4 nonsense mediated mRNA decay protein
• 2db0 hypothetical Protein

To view results, click here [5]

CATH results

CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).

To view results, click here [6]

Profunc results

The Profunc results are quite cool. Scroll down to the "cleft analysis" section, there is a good picture of how our protein can potentially bind to other proteins. to view, click here [7]

CE results CE is a structural comparison between 2 proteins. Using the zebrafish gene (PDB: 2i20) and the human Mif4g protein (PDB: 1hu3), a comparison was done. Apparently, they show more than 40% structural similarity. To find out more, click here [8]

Articles

A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery. (PDB no:1HU3) [9]

Crystal structure of the human nuclear cap binding complex. (PDB no: 1H6K) [10]

Novel eIF4G domain homologues linking mRNA translation with nonsensemediated mRNA decay [11]

• This article is quite relevant to protein function