Modomics - A Database of RNA Modifications

ID Card:

Full name: NHP2-like protein 1
Synonym: 15.5kD
GI: 2500345
COG: COG1358
UniProt: P55769
Structures: | 1E7K | 2JNB | 2OZB | 3JCR | 3SIU | 3SIV | 5O9Z | 6AH0 | 6AHD | 6QW6 | 6QX9 |
Alpha Fold Predicted Structure: AF-P55769-F1
Complex: C/D RNP


PDB Structures:


1E7K

Structure Description:

Title: Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment
Classification: RNA BINDING PROTEIN
Technique: X-Ray Diffraction
Resolution: 2.9
R value free: 0.302
R value observed: 0.216
R value work: 0.216

Abstract of the PDB Structure's related Publication:

We have determined the crystal structure of a spliceosomal RNP complex comprising the 15.5kD protein of the human U4/U6.U5 tri-snRNP and the 5' stem-loop of U4 snRNA. The protein interacts almost exclusively with a purine-rich (5+2) internal loop within the 5' stem-loop, giving an unusual RNA fold characterized by two tandem sheared G-A base pairs, a high degree of purine stacking, and the accommodation of a single RNA base, rotated out of the RNA chain, in a pocket of the protein. Apart from yielding the structure of an important entity in the pre-mRNA splicing apparatus, this work also implies a model for the complex of the 15.5kD protein with box C/D snoRNAs. It additionally suggests a general recognition principle in a novel family of RNA binding proteins.

Download RCSB-PDB Structures:

Pdb Files   1E7K.pdb   2JNB.pdb   2OZB.pdb   3JCR.pdb   3SIU.pdb   3SIV.pdb   5O9Z.pdb   6AH0.pdb   6QW6.pdb   6QX9.pdb  
Pdbx/mmCIF Files   1E7K.cif   2JNB.cif   2OZB.cif   3JCR.cif   3SIU.cif   3SIV.cif   5O9Z.cif   6AH0.cif   6AHD.cif   6QW6.cif   6QX9.cif  


Protein sequence:

MTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV

Comments:

NHP2L1 (15.5kD) protein is a homologue of yeast Snu13 and Archaea L7Ae. Binds to a common kink-turn motif of snoRNA and U4/U6, U5 splicesomal snRNA. Belongs to C/D RNP complexes acting on pre-rRNA, pre-mRNA, snRNA and a few intron-containing tRNA.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M T E A D V N P K A Y P L A D A H L T K K L L D L V Q Q S C N Y K Q L R K G A N E A T K T L N R G I S E F I V M A A D A E P L E I I L H L P L L C E D K N V P Y V F V R S K Q A L G R A C G V S R P V I A C S V T I K E G S Q L K Q Q I Q S I Q Q S I E R L L V
102030405060708090100110120MTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLVSequenceGHTBSN

Enter the variants

Position

Original

Variant

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P55769-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P55769-F1.cif  
DSSP Secondary Structures   P55769.dssp  





Publications:

Links:

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