6ZYM Splicing date Aug 02, 2020
title Human C Complex Spliceosome - High-Resolution Core
authors K.Bertram, B.Kastner
compound source
Molecule: U2 Snrna
Chain: 2
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5 Snrna
Chain: 5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna
Chain: 6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Corepressor Interacting With Rbpj 1
Chain: 9
Synonym: Cbf1-Interacting Corepressor,Recepin
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: 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: Snw Domain-Containing Protein 1
Chain: C
Synonym: Nuclear Protein Skip,Nuclear Receptor Coactivator Ski-Interacting Protein;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

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

Molecule: U5 Small Nuclear Ribonucleoprotein 40 Kda Protein
Chain: F
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: 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: Crooked Neck-Like Protein 1
Chain: O
Synonym: Crooked Neck Homolog,Hcrn
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

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

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

Molecule: Serinearginine Repetitive Matrix Protein 2
Chain: S
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: T
Synonym: Nucampholin Homolog,Fsapb
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

Molecule: Pre-Mrna
Chain: Y, Z
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Wd Repeat-Containing Protein 70
Chain: p
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Atp-Dependent Rna Helica
Chain: r
Synonym: Atp-Dependent Rna Helicase Dhx38,Deah Box Protein
Ec: 3.6.4.13
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Isy1 Homolog
Chain: s
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Splicing Factor Cwc25 Homolog
Chain: t
Synonym: Coiled-Coil Domain-Containing Protein 49,Spliceoso Associated Protein Homolog Cwc25;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor Yju2
Chain: u
Synonym: Coiled-Coil Domain-Containing Protein 94
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein Frg1
Chain: x
Synonym: Fshd Region Gene 1 Protein
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 3.40 Å
ligand GTP, IHP, MG, ZN enzyme Isomerase E.C.5.2.1.8 BRENDA
Primary referenceStructural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome., Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R, Mol Cell. 2020 Oct 1;80(1):127-139.e6. doi: 10.1016/j.molcel.2020.09.012. PMID:33007253
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (931 Kb) [Save to disk]
  • Biological Unit Coordinates (6zym.pdb1.gz) 866 Kb
  • LPC: Ligand-Protein Contacts for 6ZYM
  • CSU: Contacts of Structural Units for 6ZYM
  • Retrieve 6ZYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ZYM from S2C, [Save to disk]
    • View 6ZYM in 3D
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6ZYM
  • 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: [6zym_P] [6zym_L] [6zym_u] [6zym_9] [6zym_Q] [6zym_R] [6zym_E] [6zym_s] [6zym_S] [6zym_2] [6zym_D] [6zym_B] [6zym_Z] [6zym_T] [6zym_V] [6zym_Y] [6zym_C] [6zym_p] [6zym_5] [6zym_r] [6zym_t] [6zym_x] [6zym_O] [6zym_A] [6zym_F] [6zym_6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6ZYM
  • Community annotation for 6ZYM at PDBWiki (http://pdbwiki.org)

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