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:  
    4PKD, 4PJO

  • 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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Find proteins for P62318 (Homo sapiens)
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PHAROS:  P62318
GTEx:  ENSG00000100028
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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: SNRPB, COD, SNRPB1
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Find proteins for P14678 (Homo sapiens)
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PHAROS:  P14678
GTEx:  ENSG00000125835
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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
GTEx:  ENSG00000167088
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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: SNRPD2, SNRPD1
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PHAROS:  P62316
GTEx:  ENSG00000125743
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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
GTEx:  ENSG00000182004
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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: SNRPF, PBSCF
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PHAROS:  P62306
GTEx:  ENSG00000139343
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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: SNRPG, PBSCG
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PHAROS:  P62308
GTEx:  ENSG00000143977
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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: SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1
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Find proteins for P08621 (Homo sapiens)
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GTEx:  ENSG00000104852
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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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Find proteins for P09234 (Homo sapiens)
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GTEx:  ENSG00000124562
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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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    • Reference Sequence
    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
    Download Ideal Coordinates CCD File 
    		 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], 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] , KB [auth 2] , LB [auth 2] , OB [auth 3] , 
    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

    View Full Validation Report



    View more in-depth experimental data

    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