5H3T | pdb_00005h3t

m7G cap bound to GEMIN5-WD

• PDB DOI: https://doi.org/10.2210/pdb5H3T/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-10-27 Released: 2016-12-28 
• Deposition Author(s): Bharath, S.R., Tang, X., Song, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structural basis for specific recognition of pre-snRNA by Gemin5

Tang, X., Bharath, S.R., Piao, S., Tan, V.Q., Bowler, M.W., Song, H.

(2016) Cell Res 26: 1353-1356

• PubMed: 27834343 
• DOI: https://doi.org/10.1038/cr.2016.133
• Primary Citation Related Structures: 
  5H3S, 5H3T, 5H3U

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Organizational Affiliation: 
• Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France.
Unit of Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France.
Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 331.52 kDa 
• Atom Count: 20,448 
• Modeled Residue Count: 2,618 
• Deposited Residue Count: 2,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gem-associated protein 5	A, B, C, D	740	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGT	E [auth A], G [auth B], I [auth C], J [auth D]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C11 H20 N5 O14 P3 BUJQMJUTTBGELS-KQYNXXCUSA-N
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.159	α = 90
b = 91.007	β = 100.59
c = 153.717	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Bharath, S.R., Tang, X., Song, H.

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description