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 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1101/gad.288340.116
  • Primary Citation of Related Structures:  
    5GXH, 5GXI, 5TEE, 5TEF, 5THA

  • 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) 4-6 G]. 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 m 7 G 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 m 7 G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m 7 G 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gem-associated protein 5758Homo sapiensMutation(s): 1 
Gene Names: GEMIN5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEQ6 (Homo sapiens)
Explore Q8TEQ6 
Go to UniProtKB:  Q8TEQ6
PHAROS:  Q8TEQ6
GTEx:  ENSG00000082516 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TEQ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTG
Query on GTG

Download Ideal Coordinates CCD File 
B [auth A]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.658α = 90
b = 124.862β = 117.52
c = 60.938γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2017-05-10
    Changes: Structure summary
  • Version 1.3: 2022-12-21
    Changes: Database references
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description