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
  • Primary Citation of Related Structures:  
    4PJO, 4PKD

  • 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 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3A,
W [auth O],
L [auth a],
HA [auth o]
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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PHAROS:  P62318
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UniProt GroupP62318
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'B,
X [auth P],
M [auth b],
IA [auth p]
95Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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PHAROS:  P14678
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1C,
Y [auth Q],
N [auth c],
JA [auth q]
91Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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PHAROS:  P62314
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2D,
Z [auth R],
O [auth d],
KA [auth r]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EE,
AA [auth S],
P [auth e],
LA [auth s]
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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PHAROS:  P62304
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FF,
BA [auth T],
Q [auth f],
MA [auth t]
75Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GG,
CA [auth U],
R [auth g],
NA [auth u]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDaH [auth K],
DA [auth N],
S [auth k],
OA [auth n]
60Homo sapiensMutation(s): 0 
Gene Names: SNRNP70RNPU1ZRPU1SNRP70U1AP1
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UniProt GroupP08621
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein CI [auth L],
EA [auth M],
T [auth l],
PA [auth m]
61Homo sapiensMutation(s): 0 
Gene Names: SNRPC
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UniProt GroupP09234
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Entity ID: 10
MoleculeChainsLengthOrganismImage
U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.J [auth 1],
U [auth 2],
FA [auth 3],
QA [auth 4]
60Homo sapiens
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Entity ID: 11
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')K [auth X],
GA [auth Y],
V [auth x],
RA [auth y]
10Homo sapiens
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
HB [auth 2],
TA [auth 1]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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AC [auth y]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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FB [auth l],
NB [auth M],
SA [auth L],
UB [auth m]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

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VB [auth 4]ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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CB [auth 1],
DB [auth b],
EB [auth b],
MB [auth Q],
SB [auth 3],
CB [auth 1],
DB [auth b],
EB [auth b],
MB [auth Q],
SB [auth 3],
TB [auth 3]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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XB [auth 4]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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AB [auth 1],
BB [auth 1],
GB [auth l],
IB [auth 2],
JB [auth 2],
AB [auth 1],
BB [auth 1],
GB [auth l],
IB [auth 2],
JB [auth 2],
KB [auth 2],
LB [auth 2],
OB [auth 3],
PB [auth 3],
QB [auth 3],
RB [auth 3],
UA [auth 1],
VA [auth 1],
WA [auth 1],
WB [auth 4],
XA [auth 1],
YA [auth 1],
YB [auth y],
ZA [auth 1],
ZB [auth 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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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