3PGW Splicing Dna Rna date Nov 02, 2010
title Crystal Structure Of Human U1 Snrnp
authors G.Weber, S.Trowitzsch, B.Kastner, R.Luehrmann, M.C.Wahl
compound source
Molecule: U1-A
Chain: A, P
Synonym: U1 Snrnp A, U1 Small Nuclear Ribonucleoprotein A,
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: U1-70k
Chain: S, L
Synonym: U1 Snrnp 70 Kda, Snrnp70, U1 Small Nuclear Ribonuc 70 Kda;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm-D3
Chain: Z, W
Synonym: Small Nuclear Ribonucleoprotein Sm D3, Snrnp Core D3;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm B
Chain: B, Q
Synonym: Small Nuclear Ribonucleoprotein Polypeptides B And

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm-D1
Chain: X, U
Synonym: Small Nuclear Ribonucleoprotein Sm D1, Sm-D Autoan Snrnp Core Protein D1;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm-D2
Chain: Y, V
Synonym: Small Nuclear Ribonucleoprotein Sm D2, Snrnp Core D2;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm-F
Chain: F, I
Synonym: Snrnp-F, Sm Protein F, Small Nuclear Ribonucleopro Smf;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm-E
Chain: E, H
Synonym: Snrnp-E, Sm Protein E, Small Nuclear Ribonucleopro Sme;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Sm G
Chain: G, J
Synonym: Small Nuclear Ribonucleoprotein Polypeptide G, Iso Cra_a;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: U1 Snrna
Chain: R, N

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela

Molecule: Dna 5'-D(Apgpgptpapapgptpa)-3'
Chain: D, M
Engineered: Yes

Synthetic: Yes
Other_details: Dna Oligonucleotide
symmetry Space Group: C 1 2 1
R_factor 0.299 R_Free 0.348
crystal
cell
length a length b length c angle alpha angle beta angle gamma
358.420 88.220 150.900 90.00 111.88 90.00
method X-Ray Diffractionresolution 4.40 Å
Gene
Ontology
ChainFunctionProcessComponent
A, P

  • spliceosomal complex
  • E, H

  • catalytic step 2 spliceosome...
  • F, I

  • catalytic step 2 spliceosome...
  • J, G

  • catalytic step 2 spliceosome...
  • Q, B

  • catalytic step 2 spliceosome...
  • S, L

  • spliceosomal complex
  • X, U

  • catalytic step 2 spliceosome...
  • Y, V

  • catalytic step 2 spliceosome...
  • Z, W

  • catalytic step 2 spliceosome...
  • Primary referenceFunctional organization of the Sm core in the crystal structure of human U1 snRNP., Weber G, Trowitzsch S, Kastner B, Luhrmann R, Wahl MC, EMBO J. 2010 Dec 15;29(24):4172-84. Epub 2010 Nov 26. PMID:21113136
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3pgw.pdb1.gz) 26 Kb
  • Biological Unit Coordinates (3pgw.pdb2.gz) 26 Kb
  • CSU: Contacts of Structural Units for 3PGW
  • Structure Factors (230 Kb)
  • Retrieve 3PGW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PGW from S2C, [Save to disk]
  • View 3PGW 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 3PGW
  • 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 3PGW, from MSDmotif at EBI
  • Fold representative 3pgw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pgw_W] [3pgw_N] [3pgw_J] [3pgw_S] [3pgw_A] [3pgw_E] [3pgw_M] [3pgw_V] [3pgw] [3pgw_R] [3pgw_L] [3pgw_X] [3pgw_Z] [3pgw_I] [3pgw_G] [3pgw_B] [3pgw_U] [3pgw_Q] [3pgw_Y] [3pgw_P] [3pgw_H] [3pgw_D] [3pgw_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PGW: [RRM] [Sm ] by SMART
  • Alignments of the sequence of 3PGW with the sequences similar proteins can be viewed for 3PGW's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3PGW
  • Community annotation for 3PGW 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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