Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A5B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 91.59 kDa 
• Atom Count: 4826 
• Modelled Residue Count: 601 
• Deposited Residue Count: 808 
• Unique protein chains: 7

5XJL

Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1/D2/F/E/G from Human

• PDB DOI: 10.2210/pdb5XJL/pdb
• Entry: 5XJL supersedes: 3S6N

• Classification: SPLICING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-02 Released: 2018-05-02 
• Deposition Author(s): Zhang, R.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.296 
• R-Value Work: 0.220 
• R-Value Observed: 0.224 

Literature

Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly

Zhang, R., So, B.R., Li, P., Yong, J., Glisovic, T., Wan, L., Dreyfuss, G.

(2011) Cell 146: 384-395

• PubMed: 21816274 
• DOI: 10.1016/j.cell.2011.06.043
• Primary Citation of Related Structures:  
  5XJL


• PubMed Abstract: 
  

The SMN complex mediates the assembly of heptameric Sm protein rings on small nuclear RNAs (snRNAs), which are essential for snRNP function. Specific Sm core assembly depends on Sm proteins and snRNA recognition by SMN/Gemin2- and Gemin5-containing subunits, respectively. The mechanism by which the Sm proteins are gathered while preventing illicit Sm assembly on non-snRNAs is unknown. Here, we describe the 2.5 Å crystal structure of Gemin2 bound to SmD1/D2/F/E/G pentamer and SMN's Gemin2-binding domain, a key assembly intermediate. Remarkably, through its extended conformation, Gemin2 wraps around the crescent-shaped pentamer, interacting with all five Sm proteins, and gripping its bottom and top sides and outer perimeter. Gemin2 reaches into the RNA-binding pocket, preventing RNA binding. Interestingly, SMN-Gemin2 interaction is abrogated by a spinal muscular atrophy (SMA)-causing mutation in an SMN helix that mediates Gemin2 binding. These findings provide insight into SMN complex assembly and specificity, linking snRNP biogenesis and SMA pathogenesis.

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Organizational Affiliation: 

Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gem-associated protein 2	A [auth 2]	280	Homo sapiens	Mutation(s): 0  Gene Names: GEMIN2, SIP1
UniProt & NIH Common Fund Data Resources
Find proteins for O14893 (Homo sapiens) Explore O14893  Go to UniProtKB:  O14893
PHAROS:  O14893 GTEx:  ENSG00000092208

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D1	B [auth A]	119	Homo sapiens	Mutation(s): 0  Gene Names: SNRPD1
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens) Explore P62314  Go to UniProtKB:  P62314
PHAROS:  P62314 GTEx:  ENSG00000167088

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D2	C [auth B]	118	Homo sapiens	Mutation(s): 0  Gene Names: SNRPD2, SNRPD1
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens) Explore P62316  Go to UniProtKB:  P62316
PHAROS:  P62316 GTEx:  ENSG00000125743

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein E	D [auth E]	92	Homo sapiens	Mutation(s): 0  Gene Names: SNRPE
UniProt & NIH Common Fund Data Resources
Find proteins for P62304 (Homo sapiens) Explore P62304  Go to UniProtKB:  P62304
PHAROS:  P62304 GTEx:  ENSG00000182004

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein F	E [auth F]	86	Homo sapiens	Mutation(s): 0  Gene Names: SNRPF, PBSCF
UniProt & NIH Common Fund Data Resources
Find proteins for P62306 (Homo sapiens) Explore P62306  Go to UniProtKB:  P62306
PHAROS:  P62306 GTEx:  ENSG00000139343

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein G	F [auth G]	76	Homo sapiens	Mutation(s): 0  Gene Names: SNRPG, PBSCG
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens) Explore P62308  Go to UniProtKB:  P62308
PHAROS:  P62308 GTEx:  ENSG00000143977

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Survival motor neuron protein	G [auth M]	37	Homo sapiens	Mutation(s): 0  Gene Names: SMN1, SMN, SMNT, SMN2, SMNC
UniProt & NIH Common Fund Data Resources
Find proteins for Q16637 (Homo sapiens) Explore Q16637  Go to UniProtKB:  Q16637
PHAROS:  Q16637 GTEx:  ENSG00000172062 ENSG00000205571

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.296 
• R-Value Work: 0.220 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.83	α = 90
b = 84.6	β = 90
c = 104.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-02 
• Released Date: 2018-05-02 
Deposition Author(s): Zhang, R.
• This entry supersedes: 3S6N

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570720
National Natural Science Foundation of China	China	81441109

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release