3JCR Splicing date Jan 21, 2016
title 3d Structure Determination Of The Humanu4u6.U5 Tri-Snrnp
authors D.E.Agafonov, B.Kastner, O.Dybkov, R.V.Hofele, W.T.Liu, H.Urlaub, R.Luhrmann, H.Stark
compound source
Molecule: Hprp6
Chain: G
Synonym: Pre-Mrna-Processing Factor 6, Androgen Receptor N- Domain-Transactivating Protein 1, Ant-1, Prp6 Homolog, U5 S Associated 102 Kda Protein, U5-102 Kda Protein;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5-40k
Chain: D
Synonym: U5 Small Nuclear Ribonucleoprotein 40 Kda Protein, 40 Kda Protein, U5-40k, 38 Kda-Splicing Factor, Prp8-Bindin Hprp8bp, U5 Snrnp-Specific 40 Kda Protein, Wd Repeat-Contai Protein 57;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hbrr2
Chain: C
Synonym: U5 Small Nuclear Ribonucleoprotein 200 Kda Helicas Activating Signal Cointegrator 1 Complex Subunit 3-Like 1, Homolog, U5 Snrnp-Specific 200 Kda Protein, U5-200kd;
Ec: 3.6.4.13

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hdim1
Chain: E
Synonym: Thioredoxin-Like Protein 4a, Dim1 Protein Homolog, Spliceosomal U5 Snrnp-Specific 15 Kda Protein, Thioredoxin- Snrnp Protein U5-15kd;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hprp8
Chain: A
Synonym: Pre-Mrna-Processing-Splicing Factor 8, 220 Kda U5 Specific Protein, Prp8 Homolog, Splicing Factor Prp8, P220;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hprp28
Chain: F
Synonym: Probable Atp-Dependent Rna Helicase Ddx23, 100 Kda Specific Protein, Dead Box Protein 23, Prp28 Homolog, U5-10
Ec: 3.6.4.13

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hsnu114
Chain: B
Synonym: 116 Kda U5 Small Nuclear Ribonucleoprotein Compone Elongation Factor Tu Gtp-Binding Domain-Containing Protein Homolog, Hsnu114, U5 Snrnp-Specific Protein, 116 Kda, U5-11

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smb
Chain: O, o
Synonym: Small Nuclear Ribonucleoprotein-Associated Protein B', Snrnp-B, Sm Protein Bb', Sm-Bb', Smbb';

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smd1
Chain: P, p
Synonym: Small Nuclear Ribonucleoprotein Sm D1, Sm-D1, Sm-D Autoantigen, Snrnp Core Protein D1;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smd2
Chain: Q, q
Synonym: Small Nuclear Ribonucleoprotein Sm D2, Sm-D2, Snrn Protein D2;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smd3
Chain: R, r
Synonym: Small Nuclear Ribonucleoprotein Sm D3, Sm-D3, Snrn Protein D3;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Sme
Chain: S, s
Synonym: Small Nuclear Ribonucleoprotein E, Snrnp-E, Sm Pro Sm-E, Sme;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smf
Chain: T, t
Synonym: Small Nuclear Ribonucleoprotein F, Snrnp-F, Sm Pro Sm-F, Smf;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smg
Chain: U, u
Synonym: Small Nuclear Ribonucleoprotein G, Snrnp-G, Sm Pro Sm-G, Smg;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm8
Chain: 8
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm8

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm6
Chain: 6
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm6

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm5
Chain: 5
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm4
Chain: 4
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm4, Glycine- Protein, Grp;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm3
Chain: 3
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm3

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm2
Chain: 2
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm2, Protein Nuclear Ribonuclear Protein D Homolog, Snrnp Core Sm-Like P X5;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Lsm7
Chain: 7
Synonym: U6 Snrna-Associated Sm-Like Protein Lsm7

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hprp3
Chain: K
Synonym: U4u6 Small Nuclear Ribonucleoprotein Prp3, Pre-Mr Splicing Factor 3, Hprp3, U4u6 Snrnp 90 Kda Protein;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hprp4
Chain: L
Synonym: 60 Kda U4u6 Snrnp-Specific Spliceosomal Protein, Mrna Processing Factor 4 Homolog (Yeast), Isoform Cra_b;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hprp31
Chain: J
Synonym: U4u6 Small Nuclear Ribonucleoprotein Prp31, Pre-M Processing Factor 31, Serologically Defined Breast Cancer A Br-99, U4u6 Snrnp 61 Kda Protein, Protein 61k, Hprp31;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hsnu13
Chain: I
Synonym: Nhp2-Like Protein 1, High Mobility Group-Like Nucl Protein 2 Homolog 1, Otk27, Snu13 Homolog, Hsnu13, U4u6.U5 Nuclear Ribonucleoprotein Snu13, U4u6.U5 Tri-Snrnp 15.5 Kd Nhp2-Like Protein 1, N-Terminally Processed;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hsad1
Chain: V
Synonym: U4u6.U5 Tri-Snrnp-Associated Protein 2, Inactive Specific Peptidase 39, Sad1 Homolog, U4u6.U5 Tri-Snrnp-Ass Kda Protein, 65k;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4 Snrna
Chain: M

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna
Chain: N

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5 Snrna
Chain: H

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 7.00 Å
ligand
enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
2

  • catalytic step 2 spliceosome...
  • 3

  • catalytic step 2 spliceosome...
  • 4


    5


    6


    7


    8


    A

  • catalytic step 2 spliceosome...
  • B


    C

  • U5 snRNP
  • catalytic step 2 spliceosome...
  • D

  • catalytic step 2 spliceosome...
  • E


    F

  • U5 snRNP
  • catalytic step 2 spliceosome...
  • G
  • spliceosomal tri-snRNP compl...
  • U4/U6 x U5 tri-snRNP complex...
  • catalytic step 2 spliceosome...
  • I


    J
  • spliceosomal tri-snRNP compl...
  • U4 snRNP
  • K


    L

  • U4/U6 snRNP
  • O, o

  • catalytic step 2 spliceosome...
  • P, p

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

  • catalytic step 2 spliceosome...
  • T, t

  • catalytic step 2 spliceosome...
  • V


    q, Q

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

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

  • catalytic step 2 spliceosome...
  • Primary referenceMolecular architecture of the human U4/U6.U5 tri-snRNP., Agafonov DE, Kastner B, Dybkov O, Hofele RV, Liu WT, Urlaub H, Luhrmann R, Stark H, Science. 2016 Feb 18. pii: aad2085. PMID:26912367
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (3jcr.pdb1.gz) 187 Kb
  • CSU: Contacts of Structural Units for 3JCR
  • Retrieve 3JCR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JCR from S2C, [Save to disk]
  • View 3JCR 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 3JCR
  • 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
  • Fold representative 3jcr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jcr_S] [3jcr_H] [3jcr] [3jcr_Q] [3jcr_N] [3jcr_P] [3jcr_D] [3jcr_6] [3jcr_5] [3jcr_q] [3jcr_u] [3jcr_4] [3jcr_s] [3jcr_2] [3jcr_G] [3jcr_C] [3jcr_T] [3jcr_R] [3jcr_O] [3jcr_M] [3jcr_A] [3jcr_V] [3jcr_J] [3jcr_8] [3jcr_I] [3jcr_7] [3jcr_B] [3jcr_E] [3jcr_F] [3jcr_3] [3jcr_L] [3jcr_p] [3jcr_o] [3jcr_U] [3jcr_K] [3jcr_r] [3jcr_t]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3JCR: [AAA] [DEXDc] [DIM1] [EFG_C] [EFG_IV] [HAT] [HELICc] [JAB_MPN] [NOSIC] [PWI] [SFM] [Sec63] [Sm] [WD40] [ZnF_C2H2] [ZnF_UBP ] by SMART
  • Other resources with information on 3JCR
  • Community annotation for 3JCR at PDBWiki (http://pdbwiki.org)

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