4PJO

Minimal U1 snRNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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
  • Structures With Same Primary Citation

  • 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: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2D, R, d, r118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2, SNRPD1
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
NIH Common Fund Data Resources
PHAROS  P62316
GTEx  ENSG00000125743
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein CL, M, l, m61Homo sapiensMutation(s): 0 
Gene Names: SNRPC
Find proteins for P09234 (Homo sapiens)
Explore P09234 
Go to UniProtKB:  P09234
NIH Common Fund Data Resources
PHAROS  P09234
GTEx  ENSG00000124562
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3A, O, a, o126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
NIH Common Fund Data Resources
PHAROS  P62318
GTEx  ENSG00000100028
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'B, P, b, p95Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
NIH Common Fund Data Resources
PHAROS  P14678
GTEx  ENSG00000125835
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1C, Q, c, q91Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
NIH Common Fund Data Resources
PHAROS  P62314
GTEx  ENSG00000167088
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein EE, S, e, s92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Explore P62304 
Go to UniProtKB:  P62304
NIH Common Fund Data Resources
PHAROS  P62304
GTEx  ENSG00000182004
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein FF, T, f, t75Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
Find proteins for P62306 (Homo sapiens)
Explore P62306 
Go to UniProtKB:  P62306
NIH Common Fund Data Resources
PHAROS  P62306
GTEx  ENSG00000139343
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein GG, U, g, u76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
Find proteins for P62308 (Homo sapiens)
Explore P62308 
Go to UniProtKB:  P62308
NIH Common Fund Data Resources
PHAROS  P62308
GTEx  ENSG00000143977
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDaK, N, k, n60Homo sapiensMutation(s): 0 
Gene Names: SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1
Find proteins for P08621 (Homo sapiens)
Explore P08621 
Go to UniProtKB:  P08621
NIH Common Fund Data Resources
PHAROS  P08621
GTEx  ENSG00000104852
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

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
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 11
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')X, Y, x, y10Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download CCD File 
1, 2
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
L, M, l, m
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EOH
Query on EOH
Download CCD File 
4
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download CCD File 
1, 3, Q, b
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
4
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download CCD File 
1, 2, 3, 4, l, y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.359α = 90
b = 172.627β = 90
c = 256.322γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report


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
    Changes: Database references