1D3B

CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP DOMAIN AT 2.0A RESOLUTION

• PDB DOI:  https://doi.org/10.2210/pdb1D3B/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-12-22 Released: 1999-12-22 
• Deposition Author(s): Kambach, C., Walke, S., Avis, J.M., De La Fortelle, E., Li, J., Nagai, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.265 
• R-Value Work: 0.213 

Literature

Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.

Kambach, C., Walke, S., Young, R., Avis, J.M., de la Fortelle, E., Raker, V.A., Luhrmann, R., Li, J., Nagai, K.

(1999) Cell 96: 375-387

• PubMed: 10025403 
• DOI: https://doi.org/10.1016/s0092-8674(00)80550-4
• Primary Citation of Related Structures:  
  1B34, 1D3B


• PubMed Abstract: 
  

The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F, and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs (snRNAs). These proteins share a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Crystal structures of two Sm protein complexes, D3B and D1D2, show that these proteins have a common fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta sheet, and the D1D2 and D3B dimers superpose closely in their core regions, including the dimer interfaces. The crystal structures suggest that the seven Sm proteins could form a closed ring and the snRNAs may be bound in the positively charged central hole.

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Related Citations: 

• Structure and Assembly of the Spliceosomal Small Nuclear Ribonucleoprotein Particles
  Kambach, C., Walke, S., Nagai, K.
  (1999) Curr Opin Struct Biol 9: 222

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, England, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 115.64 kDa 
• Atom Count: 8,248 
• Modelled Residue Count: 946 
• Deposited Residue Count: 996 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)	A, C, E, G, I, K	75	Homo sapiens	Mutation(s): 1  Gene Names: SNRPD3
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens) Explore P62318  Go to UniProtKB:  P62318
PHAROS:  P62318

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)	B, D, F, H, J, L	91	Homo sapiens	Mutation(s): 0  Gene Names: SNRPB, COD, SNRPB1
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens) Explore P14678  Go to UniProtKB:  P14678
PHAROS:  P14678

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	AA [auth I], O [auth B], X [auth G]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	BA [auth I], CA [auth L], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth C], S [auth D], T [auth E], U [auth F], V [auth F], W [auth F], Y [auth G], Z [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.265 
• R-Value Work: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.35	α = 90
b = 108.45	β = 90
c = 110.42	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-22 
Deposition Author(s): Kambach, C., Walke, S., Avis, J.M., De La Fortelle, E., Li, J., Nagai, K.

Revision History  

• Version 1.0: 1999-12-22
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2011-12-07
  Changes: Database references
• Version 1.4: 2018-03-14
  Changes: Database references