4V98

The 8S snRNP Assembly Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Assembly Chaperone- Mediated snRNP Formation.

Grimm, C.Chari, A.Pelz, J.P.Kuper, J.Kisker, C.Diederichs, K.Stark, H.Schindelin, H.Fischer, U.

(2013) Mol.Cell 49: 692-703

  • DOI: 10.1016/j.molcel.2012.12.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly ch ...

    Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit. This so-called 6S complex docks subsequently onto the SMN complex, which removes pICln and enables the transfer of pre-assembled Sm proteins onto snRNA. X-ray crystallography and electron microscopy was used to investigate the structural basis of snRNP assembly. The 6S complex structure identifies pICln as an Sm protein mimic, which enables the topological organization of the Sm pentamer in a closed ring. A second structure of 6S bound to the SMN complex components SMN and Gemin2 uncovers a plausible mechanism of pICln elimination and Sm protein activation for snRNA binding. Our studies reveal how assembly factors facilitate formation of RNA-protein complexes in vivo.


    Organizational Affiliation

    Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany. clemens.grimm@uni-wuerzburg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
AI, AA, AQ, AY, Ag, Ao, Aw, BA, BI, BQ, BY, Bg, Bo, Bw, CA, CI, CQ, CY, Cg, Co
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
AJ, AB, AR, AZ, Ah, Ap, Ax, BB, BJ, BR, BZ, Bh, Bp, Bx, CB, CJ, CR, CZ, Ch, Cp
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2 (SNRPD1)
Find proteins for P62316 (Homo sapiens)
Go to Gene View: SNRPD2
Go to UniProtKB:  P62316
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
AK, AC, AS, Aa, Ai, Aq, Ay, BC, BK, BS, Ba, Bi, Bq, By, CC, CK, CS, Ca, Ci, Cq
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
AL, AD, AT, Ab, Aj, Ar, Az, BD, BL, BT, Bb, Bj, Br, Bz, CD, CL, CT, Cb, Cj, Cr
86Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
LD23602p
AM, AE, AU, Ac, Ak, As, A1, BE, BM, BU, Bc, Bk, Bs, B1, CE, CM, CU, Cc, Ck, Cs
124Drosophila melanogasterMutation(s): 0 
Gene Names: Smn
Find proteins for Q9VV74 (Drosophila melanogaster)
Go to UniProtKB:  Q9VV74
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CG10419
AN, AF, AV, Ad, Al, At, A2, BF, BN, BV, Bd, Bl, Bt, B2, CF, CN, CV, Cd, Cl, Ct
247Drosophila melanogasterMutation(s): 0 
Gene Names: Gem2
Find proteins for Q9VVX0 (Drosophila melanogaster)
Go to UniProtKB:  Q9VVX0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Icln
AO, AG, AW, Ae, Am, Au, A3, BG, BO, BW, Be, Bm, Bu, B3, CG, CO, CW, Ce, Cm, Cu
186Drosophila melanogasterMutation(s): 0 
Gene Names: icln
Find proteins for A1ZAW5 (Drosophila melanogaster)
Go to UniProtKB:  A1ZAW5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
AP, AH, AX, Af, An, Av, A4, BH, BP, BX, Bf, Bn, Bv, B4, CH, CP, CX, Cf, Cn, Cv
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A2, Ad, At, B2, Bd, BF, Bt, BV, CF, Cl
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 150.930α = 90.00
b = 356.810β = 97.31
c = 230.750γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
BUSTERrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other