5TEF

Crystal structure of Gemin5 WD40 repeats in complex with m7GpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly.

Xu, C.Ishikawa, H.Izumikawa, K.Li, L.He, H.Nobe, Y.Yamauchi, Y.Shahjee, H.M.Wu, X.H.Yu, Y.T.Isobe, T.Takahashi, N.Min, J.

(2016) Genes Dev. 30: 2376-2390

  • DOI: 10.1101/gad.288340.116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4-6G]. Gemin5, a WD40 protein component o ...

    In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4-6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gem-associated protein 5
A
758Homo sapiensMutation(s): 0 
Gene Names: GEMIN5
Find proteins for Q8TEQ6 (Homo sapiens)
Go to Gene View: GEMIN5
Go to UniProtKB:  Q8TEQ6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
GTG
Query on GTG

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Download CCD File 
A
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
MRNA CAP ANALOG N7-METHYL GPPPG
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GTGKd: 4000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 58.658α = 90.00
b = 124.862β = 117.52
c = 60.938γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-05-10
    Type: Structure summary