3CW1 Splicing date Apr 21, 2008
title Crystal Structure Of Human Spliceosomal U1 Snrnp
authors D.A.Pomeranz Krummel, C.Oubridge, A.K.Leung, J.Li, K.Nagai
compound source
Molecule: U1 Snrna
Chain: V, v, w, x
Fragment: Nucleotides 57-82 Absent, Replaced With Kissing L
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnu1a
Expression_system_vector_type: Linearized Plasmid
Expression_system_plasmid: Puc
Other_details: In Vitro Transcribed With T7 Rna Polymerase

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: D, S, T, U
Synonym: Snrnp Core Protein D3, Sm-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
Other_details: Coexpressed With Sm B, Entity 2

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei B;
Chain: A, H, I, J
Fragment: Residues 1-174
Synonym: Snrnp-B, Sm Protein Bb', Sm-Bsm-B', Smbsmb'
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Sg13009(Prep4)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe30
Other_details: Coexpressed With Sm D3, Entity 1

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: B, M, N, O
Synonym: Snrnp Core Protein D1, Sm-D1, Sm-D Autoantigen
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3, Plyss)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
Other_details: Coexpressed With Sm D2, Entity 4

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: C, P, Q, R
Synonym: Snrnp Core Protein D2, Sm-D2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3, Plyss)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
Other_details: Coexpressed With Sm D1, Entity 3

Molecule: Small Nuclear Ribonucleoprotein F
Chain: F, Z, 1, 2
Synonym: Snrnp-F, Sm Protein F, Sm-F, Smf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
Other_details: Coexpressed With Sm E And Sm G, Entities 6 A

Molecule: Small Nuclear Ribonucleoprotein E
Chain: E, W, X, Y
Synonym: Snrnp-E, Sm Protein E, Sm-E, Sme
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpe
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
Other_details: Coexpressed With Sm F And Sm G, Entities 5 A

Molecule: Small Nuclear Ribonucleoprotein G
Chain: G, 3, 4, 5
Synonym: Snrnp-G, Sm Protein G, Sm-G, Smg
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
Other_details: Coexpressed With Sm F And Sm E, Entities 5 A

Molecule: U1 Small Nuclear Ribonucleoprotein 70 Kda
Chain: K, 6, 7, 8
Fragment: Residues 1-215
Synonym: U1 Snrnp 70 Kda, Snrnp70, U1-70k
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrp70
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: U1 Small Nuclear Ribonucleoprotein C
Chain: L, 9, 0, l
Fragment: Residues 1-77
Synonym: U1 Snrnp Protein C, U1c Protein, U1-C
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3b
symmetry Space Group: P 1
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.471 127.075 152.024 95.42 105.92 101.80
method X-Ray Diffractionresolution 5.49 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
0L, 9, l


2, Z, 1, F

  • catalytic step 2 spliceosome...
  • G, 3, 4, 5

  • catalytic step 2 spliceosome...
  • K, 7, 6, 8


    N, B, M, O

  • catalytic step 2 spliceosome...
  • Q, C, P, R

  • catalytic step 2 spliceosome...
  • S, T, D, U

  • catalytic step 2 spliceosome...
  • Y, E, W, X

  • catalytic step 2 spliceosome...
  • Primary referenceCrystal structure of human spliceosomal U1 snRNP at 5.5 A resolution., Pomeranz Krummel DA, Oubridge C, Leung AK, Li J, Nagai K, Nature. 2009 Mar 26;458(7237):475-80. PMID:19325628
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (3cw1.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (3cw1.pdb2.gz) 20 Kb
  • Biological Unit Coordinates (3cw1.pdb3.gz) 20 Kb
  • Biological Unit Coordinates (3cw1.pdb4.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 3CW1
  • CSU: Contacts of Structural Units for 3CW1
  • Likely Quarternary Molecular Structure file(s) for 3CW1
  • Structure Factors (3208 Kb)
  • Retrieve 3CW1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CW1 from S2C, [Save to disk]
  • View 3CW1 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 3CW1
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3CW1, from MSDmotif at EBI
  • Fold representative 3cw1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cw1_Q] [3cw1_N] [3cw1_6] [3cw1_E] [3cw1_3] [3cw1_C] [3cw1_G] [3cw1_V] [3cw1_v] [3cw1_Z] [3cw1_9] [3cw1_A] [3cw1_P] [3cw1_4] [3cw1_W] [3cw1_Y] [3cw1_J] [3cw1_2] [3cw1_O] [3cw1_X] [3cw1_L] [3cw1_K] [3cw1_B] [3cw1_D] [3cw1_R] [3cw1_S] [3cw1] [3cw1_w] [3cw1_U] [3cw1_8] [3cw1_M] [3cw1_1] [3cw1_H] [3cw1_F] [3cw1_T] [3cw1_7] [3cw1_0] [3cw1_x] [3cw1_I] [3cw1_5] [3cw1_l]
  • SWISS-PROT database: [P14678] [P08621] [P09234] [P62304] [P62306] [P62308] [P62314] [P62316] [P62318]
  • Domain organization of [RSMB_HUMAN] [RU17_HUMAN] [RU1C_HUMAN] [RUXE_HUMAN] [RUXF_HUMAN] [RUXG_HUMAN] [SMD1_HUMAN] [SMD2_HUMAN] [SMD3_HUMAN] by SWISSPFAM
  • Domains found in 3CW1: [RRM] [Sm] [ZnF_U1 ] by SMART
  • Other resources with information on 3CW1
  • Community annotation for 3CW1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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