6FF7 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

Molecule: U2 Snrna
Chain: 2

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Bud13 Homolog
Chain: 3

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

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

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

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: 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: 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: 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

Molecule: Pre-Mrna
Chain: Z

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

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

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: Splicing Factor 3b Subunit 6
Chain: z, N
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

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3a Subunit 3
Chain: 9
Synonym: Sf3a60,Spliceosome-Associated Protein 61,Sap 61

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: Pre-Mrna-Processing Factor 19
Chain: G, H, I, J
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: 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-Splicing Factor Syf1
Chain: M
Synonym: Protein Hcnp,Xpa-Binding Protein 2

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: Intron-Binding Protein Aquarius
Chain: U
Synonym: Intron-Binding Protein Of 160 Kda,Ibp160

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein Sm D2
Chain: a, h
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
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
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
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
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
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
Synonym: Sm-D1,Sm-D Autoantigen,Snrnp Core Protein D1

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase E
Chain: o
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: Splicing Factor 3a Subunit 1
Chain: p
Synonym: Sf3a120,Spliceosome-Associated Protein 114,Sap 114

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Putative Pre-Mrna-Splicing Factor Atp-Dependent R Helicase Dhx16;
Chain: q
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

Molecule: U5 Small Nuclear Ribonucleoprotein 200 Kda Helica
Chain: r
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: Pre-Mrna-Splicing Factor Isy1 Homolog
Chain: w

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 Isomerase E.C.5.2.1.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
0


1


3


7

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

  • spliceosomal complex
  • catalytic step 2 spliceosome...
  • 9

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

  • catalytic step 2 spliceosome...
  • B


    C

  • catalytic step 2 spliceosome...
  • D

  • catalytic step 2 spliceosome...
  • E

  • catalytic step 2 spliceosome...
  • F

  • catalytic step 2 spliceosome...
  • J, H, I, G

  • catalytic step 2 spliceosome...
  • K


    L

  • catalytic step 2 spliceosome...
  • M
  • transcription, DNA-templated...
  • catalytic step 2 spliceosome...
  • N, z


    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...
  • T

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

  • catalytic step 2 spliceosome...
  • V

  • catalytic step 2 spliceosome...
  • W

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

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

  • 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

  • catalytic step 2 spliceosome...
  • p

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


    r

  • U5 snRNP
  • 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...
  • w

  • catalytic step 2 spliceosome...
  • x


    y


    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] (1842 Kb) [Save to disk]
  • Biological Unit Coordinates (6ff7.pdb1.gz) 1685 Kb
  • CSU: Contacts of Structural Units for 6FF7
  • Retrieve 6FF7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FF7 from S2C, [Save to disk]
  • View 6FF7 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 6FF7
  • 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 6ff7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ff7_8] [6ff7_1] [6ff7_z] [6ff7_9] [6ff7_O] [6ff7_D] [6ff7_h] [6ff7_B] [6ff7_x] [6ff7_s] [6ff7_y] [6ff7_j] [6ff7_I] [6ff7_Q] [6ff7_X] [6ff7_i] [6ff7_K] [6ff7_W] [6ff7_d] [6ff7_H] [6ff7_k] [6ff7_o] [6ff7_U] [6ff7_g] [6ff7_a] [6ff7_F] [6ff7_v] [6ff7_Y] [6ff7_S] [6ff7_C] [6ff7_p] [6ff7_l] [6ff7_N] [6ff7_L] [6ff7_f] [6ff7_G] [6ff7_R] [6ff7_n] [6ff7_V] [6ff7_u] [6ff7_t] [6ff7_e] [6ff7_m] [6ff7_J] [6ff7_7] [6ff7_5] [6ff7_w] [6ff7_2] [6ff7_0] [6ff7_3] [6ff7_q] [6ff7_P] [6ff7_E] [6ff7_6] [6ff7_Z] [6ff7_M] [6ff7_c] [6ff7_A] [6ff7_b] [6ff7_r] [6ff7_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FF7
  • Community annotation for 6FF7 at PDBWiki (http://pdbwiki.org)

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