4PJO Splicing date May 12, 2014
title Minimal U1 Snrnp
authors Y.Kondo, C.Oubridge, A.M.Van Roon, K.Nagai
compound source
Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: A, a, O, o
Synonym: Sm-D3,Snrnp Core Protein D3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpd3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Sg13009 (Prep4)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe30

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei B';
Chain: B, b, P, p
Synonym: Snrnp-B,Sm Protein Bb',Smbb'
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpb, Cod, Snrpb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Sg13009 (Prep4)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe30

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: C, c, Q, q
Synonym: Sm-D1,Sm-D Autoantigen,Snrnp Core Protein D1
Engineered: Yes
Mutation: Yes
Other_details: Expressed As A Fusion Protein With The N-Ter Residues Of U1-70k Protein Joined Via A (Gly-Ser)3 Linker T Terminus. This Fusion Protein Is Co-Expressed With Smd2.;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpd1
Expression_system: Escherichia Coli Bl21 (De3)
Expression_system_taxid: 469008
Expression_system_strain: Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: D, d, R, r
Synonym: Sm-D2,Snrnp Core Protein D2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpd2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Small Nuclear Ribonucleoprotein E
Chain: E, e, S, s
Synonym: Snrnp-E,Sm Protein E,Sme
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpe
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Small Nuclear Ribonucleoprotein F
Chain: F, f, T, t
Synonym: Snrnp-F,Sm Protein F,Smf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpf, Pbscf
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Small Nuclear Ribonucleoprotein G
Chain: G, g, U, u
Synonym: Snrnp-G,Sm Protein G,Smg
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpg, Pbscg
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: U1 Small Nuclear Ribonucleoprotein 70 Kda
Chain: K, k, N, n
Synonym: Snrnp70
Engineered: Yes
Mutation: Yes
Other_details: Expressed As A Fusion Protein With Smd1 (1-8 Via A (Gly-Ser)3 Linker At Its C-Terminus. This Fusion Prot Expressed With Smd2. An N-Terminal Tag Is Cleaved By Tev Pr During Purification, Leaving An N-Terminal Gly Residue.;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrnp70, Rnpu1z, Rpu1, Snrp70, U1ap1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: U1 Small Nuclear Ribonucleoprotein C
Chain: L, l, M, m
Synonym: U1c
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpc
Expression_system: Escherichia Coli B
Expression_system_taxid: 37762
Expression_system_strain: B834 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3b

Molecule: U1 Rna Variant (48-Mer) With 4-Helix Junction Rep Kissing Loop (Hiv-1 (Mal) Dis) And Shorter Stem-Loop 4.;
Chain: 1, 2, 3, 4
Engineered: Yes
Other_details: Made By In Vitro Transcription Using T7 Rna From A Linearised Puc Plasmid Template Containing A T7 Prom Followed By The Template Sequence.;

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna (5'-R(Apgpgpupapapgpupcpc)-3')
Chain: X, x, Y, y
Engineered: Yes
Other_details: Rna Made By Chemical Synthesis. Sequence Bas Consensus Human 5' Splice Site.

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.359 172.627 256.322 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand CL, EOH, EPE, GTP, K, MG, SO4, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, T, f, t


M, L, m, l


Q, C, c, q


S, E, e, s

  • catalytic step 2 spliceosome...
  • a, A, O, o

  • catalytic step 2 spliceosome...
  • r, d, D, R

  • catalytic step 2 spliceosome...
  • u, g, G, U

  • catalytic step 2 spliceosome...
  • Primary referenceCrystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition., Kondo Y, Oubridge C, van Roon AM, Nagai K, Elife. 2015 Jan 2;4. doi: 10.7554/eLife.04986. PMID:25555158
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (563 Kb) [Save to disk]
  • Biological Unit Coordinates (4pjo.pdb1.gz) 145 Kb
  • Biological Unit Coordinates (4pjo.pdb2.gz) 142 Kb
  • Biological Unit Coordinates (4pjo.pdb3.gz) 143 Kb
  • Biological Unit Coordinates (4pjo.pdb4.gz) 145 Kb
  • LPC: Ligand-Protein Contacts for 4PJO
  • CSU: Contacts of Structural Units for 4PJO
  • Structure Factors (4221 Kb)
  • Retrieve 4PJO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PJO from S2C, [Save to disk]
  • Re-refined 4pjo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PJO in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4PJO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4PJO, from MSDmotif at EBI
  • Fold representative 4pjo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pjo_L] [4pjo_P] [4pjo_d] [4pjo_Y] [4pjo_N] [4pjo_M] [4pjo] [4pjo_E] [4pjo_y] [4pjo_u] [4pjo_R] [4pjo_e] [4pjo_t] [4pjo_p] [4pjo_K] [4pjo_c] [4pjo_T] [4pjo_x] [4pjo_D] [4pjo_r] [4pjo_U] [4pjo_n] [4pjo_G] [4pjo_F] [4pjo_X] [4pjo_s] [4pjo_q] [4pjo_m] [4pjo_C] [4pjo_l] [4pjo_a] [4pjo_A] [4pjo_k] [4pjo_o] [4pjo_b] [4pjo_S] [4pjo_O] [4pjo_g] [4pjo_Q] [4pjo_f] [4pjo_3] [4pjo_2] [4pjo_B] [4pjo_4] [4pjo_1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4PJO: [Sm] [ZnF_U1 ] by SMART
  • Other resources with information on 4PJO
  • Community annotation for 4PJO at PDBWiki (http://pdbwiki.org)

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