5Z58 Splicing date Jan 17, 2018
title Cryo-Em Structure Of A Human Activated Spliceosome (Early Ba Angstrom.
authors X.Zhang, C.Yan, X.Zhan, L.Li, J.Lei, Y.Shi
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: U5 Snrna
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 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

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: Small Nuclear Ribonucleoprotein Sm D3
Chain: a, h
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: b, I
Synonym: Snrnp-B,Sm Protein Bb',Smbb'

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D1
Chain: c, j
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: d, k
Synonym: Sm-D2,Snrnp Core Protein D2

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein F
Chain: f, m
Synonym: Snrnp-F,Sm Protein F,Smf

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein E
Chain: e, l
Synonym: Snrnp-E,Sm Protein E,Sme

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein G
Chain: g, n
Synonym: Snrnp-G,Sm Protein G,Smg

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna
Chain: F

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified Adenovirus
Organism_taxid: 10535

Molecule: U2 Snrna
Chain: H

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: Splicing Factor 3a Subunit 3
Chain: w
Synonym: Sf3a60,Spliceosome-Associated Protein 61,Sap 61

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3a Subunit 1
Chain: u
Synonym: Sf3a120,Spliceosome-Associated Protein 114,Sap 114

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3a Subunit 2
Chain: v
Synonym: Sf3a66,Spliceosome-Associated Protein 62,Sap 62

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 1
Chain: 1
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 2
Chain: 2
Synonym: Pre-Mrna-Splicing Factor Sf3b 145 Kda Subunit,Sf3b Spliceosome-Associated Protein 145,Sap 145;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 3
Chain: 3
Synonym: Sf3b135, Pre-Mrna-Splicing Factor Sf3b 130 Kda Sub Sf3b130,Staf130,Spliceosome-Associated Protein 130,Sap 130;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 4
Chain: 4
Synonym: Pre-Mrna-Splicing Factor Sf3b 49 Kda Subunit,Splic Associated Protein 49,Sap 49;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 6
Chain: 5
Synonym: Sf3b14b, Pre-Mrna Branch Site Protein P14,Sf3b 14 Subunit,Sf3b14a,Spliceosome-Associated Protein,14-Kda,Splic 3b,Subunit 6,14kda;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Phd Finger-Like Domain-Containing Protein 5a
Chain: 6
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: Splicing Factor 3b Subunit 5
Chain: 7
Synonym: Sf3b5,Pre-Mrna-Splicing Factor Sf3b 10 Kda Subunit

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Crooked Neck-Like Protein 1
Chain: J
Synonym: Syf3, 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: Ring Finger Protein 113a
Chain: M
Synonym: Zinc Finger Protein 183

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: Skip
Chain: R

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: Pre-Mrna-Splicing Factor Cwc22 Homolog
Chain: V
Synonym: Nucampholin Homolog,Fsapb

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Smad Nuclear-Interacting Protein 1
Chain: X
Synonym: Fha Domain-Containing Protein Snip1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna-Binding Motif Protein, X-Linked 2
Chain: Y

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Bud13 Homolog
Chain: Z

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase Cwc27 Homolog
Chain: z
Synonym: Ppiase Cwc27,Antigen Ny-Co-10,Serologically Define Cancer Antigen 10;
Ec: 5.2.1.8

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Atp-Dependent Rna Helica
Chain: x
Synonym: Atp-Dependent Rna Helicase #3,Deah-Box Protein 16
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 4.90 Å
ligand GTP, IHP, MG, ZN enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1
  • splicing factor binding

  • catalytic step 2 spliceosome...
  • 2

  • spliceosomal complex
  • catalytic step 2 spliceosome...
  • 3
  • protein binding

  • catalytic step 2 spliceosome...
  • 4

  • spliceosomal complex
  • 5


    6


    7


    A
  • metallopeptidase activity
  • isopeptidase activity

  • catalytic step 2 spliceosome...
  • C


    D

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

  • catalytic step 2 spliceosome...
  • J

  • catalytic step 2 spliceosome...
  • L

  • catalytic step 2 spliceosome...
  • M


    P

  • catalytic step 2 spliceosome...
  • R


    T

  • catalytic step 2 spliceosome...
  • V

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


    Y


    Z


    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...
  • u

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

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

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


    z

  • U2-type precatalytic spliceo...
  • catalytic step 2 spliceosome...
  • Primary referenceStructure of the human activated spliceosome in three conformational states., Zhang X, Yan C, Zhan X, Li L, Lei J, Shi Y, Cell Res. 2018 Mar;28(3):307-322. doi: 10.1038/cr.2018.14. Epub 2018 Jan 23. PMID:29360106
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2018 Kb) [Save to disk]
  • Biological Unit Coordinates (5z58.pdb1.gz) 1915 Kb
  • LPC: Ligand-Protein Contacts for 5Z58
  • CSU: Contacts of Structural Units for 5Z58
  • Retrieve 5Z58 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Z58 from S2C, [Save to disk]
  • View 5Z58 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 5Z58
  • 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 5z58 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5z58_p] [5z58_i] [5z58_b] [5z58_T] [5z58_7] [5z58_f] [5z58_g] [5z58_o] [5z58_u] [5z58_e] [5z58_L] [5z58_5] [5z58_w] [5z58_R] [5z58_a] [5z58_M] [5z58_x] [5z58_P] [5z58_Z] [5z58_k] [5z58_z] [5z58_l] [5z58_2] [5z58_D] [5z58_V] [5z58_A] [5z58_m] [5z58_B] [5z58_v] [5z58_E] [5z58_3] [5z58_X] [5z58_1] [5z58_6] [5z58_J] [5z58_Y] [5z58_F] [5z58_4] [5z58_d] [5z58_n] [5z58_G] [5z58_C] [5z58_j] [5z58_c] [5z58_h] [5z58_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Z58
  • Community annotation for 5Z58 at PDBWiki (http://pdbwiki.org)

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