6ICZ Splicing date Sep 07, 2018
title Cryo-Em Structure Of A Human Post-Catalytic Spliceosome (P C 3.0 Angstrom
authors X.Zhang, X.Zhan, C.Yan, Y.Shi
compound source
Molecule: Protein Mago Nashi Homolog 2
Chain: v
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna-Binding Protein 8a
Chain: w
Synonym: Binder Of Ovca1-1,Bov-1,Rna-Binding Motif Protein Binding Protein Y14,Ribonucleoprotein Rbm8a;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Eukaryotic Initiation Factor 4a-III
Chain: u
Synonym: Eif4a-III,Atp-Dependent Rna Helicase Ddx48,Atp-Dep Helicase Eif4a-3,Dead Box Protein 48,Eukaryotic Initiation Like Nuk-34,Eukaryotic Translation Initiation Factor 4a Iso Nuclear Matrix Protein 265,Hnmp 265;
Ec: 3.6.4.13
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein Casc3
Chain: x
Synonym: Cancer Susceptibility Candidate Gene 3 Protein,Met Lymph Node Gene 51 Protein,Mln 51,Protein Barentsz,Btz;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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: U5snrna
Chain: B
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: 116 Kda U5 Small Nuclear Ribonucleoprotein Compon
Chain: C
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 40 Kda Protein
Chain: E
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: U6snrna
Chain: F
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna
Chain: G
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2snrna
Chain: H
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Crooked Neck-Like Protein 1
Chain: J
Synonym: Crooked Neck Homolog,Hcrn
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Cell Division Cycle 5-Like Protein
Chain: L
Synonym: Cdc5-Like Protein,Pombe Cdc5-Related Protein
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Syf2
Chain: M
Synonym: Ccndbp1-Interactor,P29
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein Bud31 Homolog
Chain: N
Synonym: Protein Edg-2,Protein G10 Homolog
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Rbm22
Chain: O
Synonym: Rna-Binding Motif Protein 22,Zinc Finger Ccch Doma Containing Protein 16;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Spliceosome-Associated Protein Cwc15 Homolog
Chain: P
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Snw Domain-Containing Protein 1
Chain: R
Synonym: Nuclear Protein Skip,Nuclear Receptor Coactivator Ski-Interacting Protein;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase-Like 1
Chain: S
Synonym: Ppiase,Rotamase Ppil1
Ec: 5.2.1.8
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pleiotropic Regulator 1
Chain: T
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Serinearginine Repetitive Matrix Protein 2
Chain: U
Synonym: 300 Kda Nuclear Matrix Antigen,Serinearginine-Ric Factor-Related Nuclear Matrix Protein Of 300 Kda,Serarg-Re Nuclear Matrix Protein Of 300 Kda,Splicing Coactivator Subu Srm300,Tax-Responsive Enhancer Element-Binding Protein 803,
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Cwc22 Homolog
Chain: V
Synonym: Nucampholin Homolog,Fsapb
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Processing Factor 17
Chain: W
Synonym: Cell Division Cycle 40 Homolog,Eh-Binding Protein Prp17 Homolog,Hprp17;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Prkr-Interacting Protein 1
Chain: X
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Slu7
Chain: Z
Synonym: Hslu7
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Syf1
Chain: I
Synonym: Protein Hcnp,Xpa-Binding Protein 2
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase E
Chain: y
Synonym: Ppiase E,Cyclophilin E,Cyclophilin-33,Rotamase E
Ec: 5.2.1.8
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna Helicase Aquarius
Chain: Q
Synonym: Intron-Binding Protein Of 160 Kda,Ibp160
Ec: 3.6.4.13
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: h, a
Synonym: Sm-D3,Snrnp Core Protein D3
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein-Associated Protei
Chain: I, b
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: j, c
Synonym: Sm-D1,Sm-D Autoantigen,Snrnp Core Protein D1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: k, d
Synonym: Sm-D2,Snrnp Core Protein D2
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein F
Chain: m, f
Synonym: Snrnp-F,Sm Protein F,Smf
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein E
Chain: l, e
Synonym: Snrnp-E,Sm Protein E,Sme
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein G
Chain: n, g
Synonym: Snrnp-G,Sm Protein G,Smg
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2 Small Nuclear Ribonucleoprotein A'
Chain: o
Synonym: U2 Snrnp A'
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2 Small Nuclear Ribonucleoprotein B''
Chain: p
Synonym: U2 Snrnp B''
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Atp-Dependent Rna Helicase Dhx8
Chain: Y
Synonym: Deah Box Protein 8,Rna Helicase Hrh1
Ec: 3.6.4.13
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Spf27
Chain: K
Synonym: Breast Carcinoma-Amplified Sequence 2,Dna Amplifie Mammary Carcinoma 1 Protein,Spliceosome-Associated Protein
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Processing Factor 19
Chain: q, r, s, t
Synonym: Nuclear Matrix Protein 200,Prp19pso4 Homolog,Hpso Type E3 Ubiquitin Transferase Prp19,Senescence Evasion Fact
Ec: 2.3.2.27
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5 Small Nuclear Ribonucleoprotein 200 Kda Helica
Chain: D
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
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 3.00 Å
ligand ATP, GTP, IHP, MG, SEP, ZN enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • metallopeptidase activity
  • isopeptidase activity

  • catalytic step 2 spliceosome...
    • C


    D

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

  • catalytic step 2 spliceosome...
    • I
  • transcription, DNA-templated...
  • catalytic step 2 spliceosome...
    • J

  • catalytic step 2 spliceosome...
    • K


    L

  • catalytic step 2 spliceosome...
    • M

  • catalytic step 2 spliceosome...
    • N
  • ligand-dependent nuclear rec...


    • O

  • catalytic step 2 spliceosome...
    • P

  • catalytic step 2 spliceosome...
    • Q

  • catalytic step 2 spliceosome...
    • R

  • catalytic step 2 spliceosome...
    • S

  • catalytic step 2 spliceosome...
    • T

  • catalytic step 2 spliceosome...
    • U

  • catalytic step 2 spliceosome...
    • V

  • spliceosomal complex
  • catalytic step 2 spliceosome...
    • W

  • catalytic step 2 spliceosome...
    • X


    Y

  • catalytic step 2 spliceosome...
    • Z

  • catalytic step 2 spliceosome...
    • a, h

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

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

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

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

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

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

  • catalytic step 2 spliceosome...
    • o

  • spliceosomal complex
  • catalytic step 2 spliceosome...
    • p

  • spliceosomal complex
  • U2 snRNP
  • catalytic step 2 spliceosome...
    • t, s, q, r

  • catalytic step 2 spliceosome...
    • u

  • catalytic step 2 spliceosome...
    • v


    w

  • catalytic step 2 spliceosome...
    • x


    y

  • catalytic step 2 spliceosome...
    • Primary referenceStructures of the human spliceosomes before and after release of the ligated exon., Zhang X, Zhan X, Yan C, Zhang W, Liu D, Lei J, Shi Y, Cell Res. 2019 Feb 6. pii: 10.1038/s41422-019-0143-x. doi:, 10.1038/s41422-019-0143-x. PMID:30728453
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1961 Kb) [Save to disk]
  • Biological Unit Coordinates (6icz.pdb1.gz) 1833 Kb
  • LPC: Ligand-Protein Contacts for 6ICZ
  • CSU: Contacts of Structural Units for 6ICZ
  • Retrieve 6ICZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ICZ from S2C, [Save to disk]
    • View 6ICZ 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 6ICZ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6icz_q] [6icz_F] [6icz_L] [6icz_B] [6icz_D] [6icz_X] [6icz_i] [6icz_w] [6icz_C] [6icz_u] [6icz_Y] [6icz_N] [6icz_k] [6icz_U] [6icz_f] [6icz_o] [6icz_S] [6icz_H] [6icz_d] [6icz_m] [6icz_O] [6icz_c] [6icz_x] [6icz_V] [6icz_e] [6icz_P] [6icz_M] [6icz_W] [6icz_Z] [6icz_v] [6icz_b] [6icz_p] [6icz_r] [6icz_t] [6icz_Q] [6icz_R] [6icz_K] [6icz_l] [6icz_s] [6icz_E] [6icz_G] [6icz_y] [6icz_g] [6icz_I] [6icz_h] [6icz_n] [6icz_a] [6icz_T] [6icz_j] [6icz_A] [6icz_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6ICZ
  • Community annotation for 6ICZ at PDBWiki (http://pdbwiki.org)

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