4PJO

Minimal U1 snRNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.

Kondo, Y., Oubridge, C., van Roon, A.M., Nagai, K.

(2015) Elife 4: --

  • DOI: 10.7554/eLife.04986
  • Primary Citation of Related Structures:  
  • Also Cited By: 4WZJ

  • PubMed Abstract: 

    • U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost co ...

    U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost complete network of protein-protein and RNA-protein interactions within U1 snRNP, and show how the 5' splice site of pre-mRNA is recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between pre-mRNA and the 5'-end of U1 snRNA. The binding of the RNA duplex is stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts with pre-mRNA. The structure, together with RNA binding assays, shows that the selection of 5'-splice site nucleotides by U1 snRNP is achieved predominantly through basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched 5'-splice sites.

    Organizational Affiliation: 

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
A, a, O, o
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
B, b, P, p
95Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
C, c, Q, q
91Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
D, d, R, r
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: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
E, e, S, s
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
F, f, T, t
75Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
G, g, U, u
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa
K, k, N, n
60Homo sapiensMutation(s): 0 
Gene Names: SNRNP70 (RNPU1Z, RPU1, SNRP70, U1AP1)
Find proteins for P08621 (Homo sapiens)
Go to Gene View: SNRNP70
Go to UniProtKB:  P08621
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
L, l, M, m
61Homo sapiensMutation(s): 0 
Gene Names: SNRPC
Find proteins for P09234 (Homo sapiens)
Go to Gene View: SNRPC
Go to UniProtKB:  P09234
Entity ID: 10
MoleculeChainsLengthOrganism
U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.1,2,3,460Homo sapiens
Entity ID: 11
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')X,x,Y,y10Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
1, 3, b, Q
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE
Download SDF File 
Download CCD File 
1, 2
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
l, L, m, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
4
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
1, 2, 3, 4, l, y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH
Download SDF File 
Download CCD File 
4
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
1, 2, 3, 4
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.359α = 90.00
b = 172.627β = 90.00
c = 256.322γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
Cootmodel building
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references