5O9Z Splicing date Jun 20, 2017
title Cryo-Em Structure Of A Pre-Catalytic Human Spliceosome Prime Activation (B Complex)
authors K.Bertram, B.Kastner
compound source
Molecule: Pre-Mrna-Processing-Splicing Factor 8
Chain: A
Synonym: 220 Kda U5 Snrnp-Specific Protein,Prp8 Homolog,Spl Factor Prp8,P220;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 116 Kda U5 Small Nuclear Ribonucleoprotein Compon
Chain: B
Synonym: Elongation Factor Tu Gtp-Binding Domain-Containing 2,Snu114 Homolog,Hsnu114,U5 Snrnp-Specific Protein,116 Kda, Kda;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5 Small Nuclear Ribonucleoprotein 200 Kda Helica
Chain: C
Synonym: Activating Signal Cointegrator 1 Complex Subunit 3 Brr2 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: U5 Small Nuclear Ribonucleoprotein 40 Kda Protein
Chain: D
Synonym: U5-40k,38 Kda-Splicing Factor,Prp8-Binding Protein U5 Snrnp-Specific 40 Kda Protein,Wd Repeat-Containing Prote

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp3
Chain: E
Synonym: Pre-Mrna-Splicing Factor 3,Hprp3,U4u6 Snrnp 90 Kd

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp4
Chain: F
Synonym: Prp4 Homolog,Hprp4,U4u6 Snrnp 60 Kda Protein,Wd S Factor Prp4;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Processing Factor 6
Chain: G
Synonym: Androgen Receptor N-Terminal Domain-Transactivatin 1,Ant-1,Prp6 Homolog,U5 Snrnp-Associated 102 Kda Protein,U5 Protein;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp31
Chain: H
Synonym: Pre-Mrna-Processing Factor 31,Serologically Define Cancer Antigen Ny-Br-99,U4u6 Snrnp 61 Kda Protein,Hprp31;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor 38a
Chain: I

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Thioredoxin-Like Protein 4a
Chain: J
Synonym: Dim1 Protein Homolog,Spliceosomal U5 Snrnp-Specifi Protein,Thioredoxin-Like U5 Snrnp Protein U5-15kd;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Microfibrillar-Associated Protein 1
Chain: K

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Wd40 Repeat-Containing Protein Smu1
Chain: L
Synonym: Smu-1 Suppressor Of Mec-8 And Unc-52 Protein Homol

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase H
Chain: M
Synonym: Ppiase H,Rotamase H,Small Nuclear Ribonucleoprotei Particle-Specific Cyclophilin H,Cyph,U-Snrnp-Associated Cyc Snucyp-20,Usa-Cyp;
Ec: 5.2.1.8

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Zinc Finger Matrin-Type Protein 2
Chain: N

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nhp2-Like Protein 1
Chain: O
Synonym: High Mobility Group-Like Nuclear Protein 2 Homolog Snu13 Homolog,Hsnu13,U4u6.U5 Small Nuclear Ribonucleoprote U4u6.U5 Tri-Snrnp 15.5 Kda Protein;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6.U5 Tri-Snrnp-Associated Protein 1
Chain: P
Synonym: Snu66 Homolog,Hsnu66,Squamous Cell Carcinoma Antig Recognized By T-Cells 1,Hsart-1,U4u6.U5 Tri-Snrnp-Associat Protein;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Ww Domain-Binding Protein 4
Chain: Q
Synonym: Wbp-4,Formin-Binding Protein 21,Ww Domain-Containi Protein 4;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein Red
Chain: R
Synonym: Cytokine Ik,Ik Factor,Protein Rer

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: a, h, S
Synonym: Sm-D2,Snrnp Core Protein D2

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein F
Chain: b, I, T
Synonym: Snrnp-F,Sm Protein F,Smf

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein E
Chain: c, j, U
Synonym: Snrnp-E,Sm Protein E,Sme

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein G
Chain: d, k, V
Synonym: Snrnp-G,Sm Protein G,Smg

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: e, l, W
Synonym: Sm-D3,Snrnp Core Protein D3

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei B';
Chain: f, m, X
Synonym: Snrnp-B,Sm Protein Bb',Smbb'

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: g, n, Z
Synonym: Sm-D1,Sm-D Autoantigen,Snrnp Core Protein D1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm2
Chain: o
Synonym: Protein G7b,Small Nuclear Ribonuclear Protein D Ho Snrnp Core Sm-Like Protein Sm-X5;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm3
Chain: p

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm4
Chain: q
Synonym: Glycine-Rich Protein,Grp

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm5
Chain: r

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm6
Chain: s

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm7
Chain: t

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm8
Chain: u

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 1
Chain: v
Synonym: Pre-Mrna-Splicing Factor Sf3b 155 Kda Subunit,Sf3b Spliceosome-Associated Protein 155,Sap 155;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 3 (Sf3b3)
Chain: w

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 5
Chain: x
Synonym: Sf3b5,Pre-Mrna-Splicing Factor Sf3b 10 Kda Subunit

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Phd Finger-Like Domain-Containing Protein 5a
Chain: y
Synonym: Phd Finger-Like Domain Protein 5a,Splicing Factor Associated 14 Kda Protein,Sf3b14b;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2 Small Nuclear Ribonucleoprotein A'
Chain: z
Synonym: U2 Snrnp A'

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2 Small Nuclear Ribonucleoprotein B''
Chain: 1
Synonym: U2 Snrnp B''

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Minx Pre-Mrna
Chain: Y

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Human Gene For Small Nuclear Rna U2 (Snrna U2)
Chain: 2

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Homo Sapiens U4a Snrna
Chain: 4

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Homo Sapiens U5 A Small Nuclear Rna
Chain: 5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Homo Sapiens Rna, U6 Small Nuclear 1 (Rnu6-1), Sm Nuclear Rna;
Chain: 6

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 4.50 Å
ligand
enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1

  • spliceosomal complex
  • U2 snRNP
  • catalytic step 2 spliceosome...
  • A

  • catalytic step 2 spliceosome...
  • B


    C

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

  • catalytic step 2 spliceosome...
  • E


    F

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


    J


    K


    L


    M

  • U4/U6 x U5 tri-snRNP complex...
  • U4/U6 snRNP
  • N


    O


    P

  • catalytic step 2 spliceosome...
  • Q


    R


    S, a, h

  • catalytic step 2 spliceosome...
  • T, b, i

  • catalytic step 2 spliceosome...
  • Z, g, n

  • catalytic step 2 spliceosome...
  • d, k, V

  • catalytic step 2 spliceosome...
  • e, W, l

  • catalytic step 2 spliceosome...
  • f, X, m

  • catalytic step 2 spliceosome...
  • j, c, U

  • catalytic step 2 spliceosome...
  • o

  • catalytic step 2 spliceosome...
  • p

  • catalytic step 2 spliceosome...
  • q


    r


    s


    t


    u


    v

  • catalytic step 2 spliceosome...
  • w

  • catalytic step 2 spliceosome...
  • x


    y


    Primary referenceCryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation., Bertram K, Agafonov DE, Dybkov O, Haselbach D, Leelaram MN, Will CL, Urlaub H, Kastner B, Luhrmann R, Stark H, Cell. 2017 Aug 10;170(4):701-713.e11. doi: 10.1016/j.cell.2017.07.011. Epub 2017 , Aug 3. PMID:28781166
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1115 Kb) [Save to disk]
  • Biological Unit Coordinates (5o9z.pdb1.gz) 1035 Kb
  • CSU: Contacts of Structural Units for 5O9Z
  • Retrieve 5O9Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5O9Z from S2C, [Save to disk]
  • View 5O9Z 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 5O9Z
  • 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 5o9z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5o9z_Y] [5o9z_H] [5o9z_D] [5o9z_Q] [5o9z_a] [5o9z_6] [5o9z_E] [5o9z_c] [5o9z_P] [5o9z_i] [5o9z_O] [5o9z_g] [5o9z_M] [5o9z_G] [5o9z_L] [5o9z_4] [5o9z_W] [5o9z_n] [5o9z_h] [5o9z_f] [5o9z_o] [5o9z_I] [5o9z_q] [5o9z_l] [5o9z_T] [5o9z_S] [5o9z_z] [5o9z_X] [5o9z_J] [5o9z_w] [5o9z_r] [5o9z_e] [5o9z_R] [5o9z_j] [5o9z_N] [5o9z_s] [5o9z_F] [5o9z_x] [5o9z_2] [5o9z_U] [5o9z_K] [5o9z_C] [5o9z_p] [5o9z_d] [5o9z_m] [5o9z_v] [5o9z_t] [5o9z_B] [5o9z_1] [5o9z_Z] [5o9z_u] [5o9z_y] [5o9z_k] [5o9z_b] [5o9z_5] [5o9z_V] [5o9z_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5O9Z
  • Community annotation for 5O9Z at PDBWiki (http://pdbwiki.org)

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