6FF4 Splicing date Jan 03, 2018
title Human Bact Spliceosome Core Structure
authors D.Haselbach, I.Komarov, D.Agafonov, K.Hartmuth, B.Graf, B.Kastner R.Luehrmann, H.Stark
compound source
Molecule: Rna-Binding Motif Protein, X-Linked 2
Chain: 1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: U2 Snrna
Chain: 2

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Bud13 Homolog
Chain: 3

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: U5 Snrna
Chain: 5

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: U6 Snrna
Chain: 6

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Splicing Factor 3a Subunit 2
Chain: 7
Synonym: Sf3a66,Spliceosome-Associated Protein 62,Sap 62

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Splicing Factor 3b Subunit 2
Chain: 8
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
Cell_line: Hela S3

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
Cell_line: Hela S3

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
Cell_line: Hela S3

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
Cell_line: Hela S3

Molecule: Pleiotropic Regulator 1
Chain: D

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

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
Cell_line: Hela S3

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
Cell_line: Hela S3

Molecule: Crooked Neck-Like Protein 1
Chain: O
Synonym: Crooked Neck Homolog,Hcrn

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

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
Cell_line: Hela S3

Molecule: Protein Bud31 Homolog
Chain: Q
Synonym: Protein Edg-2,Protein G10 Homolog

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Spliceosome-Associated Protein Cwc15 Homolog
Chain: R

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

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
Cell_line: Hela S3

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
Cell_line: Hela S3

Molecule: Serinearginine Repetitive Matrix Protein 1
Chain: Y
Synonym: Sr-Related Nuclear Matrix Protein Of 160 Kda,Srm16 Related Nuclear Matrix Protein;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Pre Mrna
Chain: Z

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase Cwc27 Homolog
Chain: s
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
Cell_line: Hela S3

Molecule: Ring Finger Protein 113a
Chain: t
Synonym: Zinc Finger Protein 183

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

Molecule: Splicing Factor 3b Subunit 1
Chain: u
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
Cell_line: Hela S3

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3

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
Cell_line: Hela S3

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
Cell_line: Hela S3

Molecule: Splicing Factor 3b Subunit 6
Chain: z
Synonym: Pre-Mrna Branch Site Protein P14,Sf3b 14 Kda Subun Sf3b14a,Spliceosome-Associated Protein,14-Kda,Splicing Fact Subunit 6,14kda

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela S3
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
Gene
Ontology
ChainFunctionProcessComponent
1


3


7

  • spliceosomal complex
  • catalytic step 2 spliceosome...
  • 8

  • spliceosomal complex
  • catalytic step 2 spliceosome...
  • A
  • metallopeptidase activity
  • isopeptidase activity

  • catalytic step 2 spliceosome...
  • B


    C

  • catalytic step 2 spliceosome...
  • D

  • catalytic step 2 spliceosome...
  • E

  • catalytic step 2 spliceosome...
  • L

  • catalytic step 2 spliceosome...
  • O

  • catalytic step 2 spliceosome...
  • P

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


  • R

  • catalytic step 2 spliceosome...
  • S

  • catalytic step 2 spliceosome...
  • V

  • catalytic step 2 spliceosome...
  • Y

  • catalytic step 2 spliceosome...
  • s

  • U2-type precatalytic spliceo...
  • catalytic step 2 spliceosome...
  • t


    u
  • splicing factor binding

  • catalytic step 2 spliceosome...
  • v
  • protein binding

  • catalytic step 2 spliceosome...
  • x


    y


    z


    Primary referenceStructure and Conformational Dynamics of the Human Spliceosomal B(act) Complex., Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luhrmann R, Stark H, Cell. 2018 Jan 25;172(3):454-464.e11. doi: 10.1016/j.cell.2018.01.010. Epub 2018 , Jan 17. PMID:29361316
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1360 Kb) [Save to disk]
  • Biological Unit Coordinates (6ff4.pdb1.gz) 1289 Kb
  • LPC: Ligand-Protein Contacts for 6FF4
  • CSU: Contacts of Structural Units for 6FF4
  • Retrieve 6FF4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FF4 from S2C, [Save to disk]
  • View 6FF4 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 6FF4
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n6ff4, region F:680-762,F:854-1061 [Jmol] [rasmolscript] [script source]
  • Fold representative 6ff4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ff4_v] [6ff4_A] [6ff4_O] [6ff4_D] [6ff4_C] [6ff4_u] [6ff4_E] [6ff4_2] [6ff4_1] [6ff4_6] [6ff4_V] [6ff4_Z] [6ff4_x] [6ff4_3] [6ff4_y] [6ff4_7] [6ff4_S] [6ff4_z] [6ff4_t] [6ff4_B] [6ff4_8] [6ff4_5] [6ff4_s] [6ff4_R] [6ff4_L] [6ff4_Q] [6ff4_P] [6ff4_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FF4
  • Community annotation for 6FF4 at PDBWiki (http://pdbwiki.org)

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