5MQF Splicing date Dec 20, 2016
title Cryo-Em Structure Of A Human Spliceosome Activated For Step Splicing (C Complex)
authors K.Bertram, K.Hartmuth, B.Kastner
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: 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: Pre-Mrna-Processing Factor 19
Chain: G, H, I, J
Synonym: Nuclear Matrix Protein 200,Prp19pso4 Homolog,Hpso Senescence Evasion Factor;
Ec: 6.3.2.-

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: 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 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 Syf2
Chain: N
Synonym: Ccndbp1-Interactor,P29

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: 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: 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: 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: Eukaryotic Initiation Factor 4a-III
Chain: p
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: Atp-Dependent Rna Helicase Dhx8
Chain: q
Synonym: Deah Box Protein 8,Rna Helicase Hrh1
Ec: 3.6.4.13

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Minx Pre-Mrna (Intron)
Chain: Y, Z

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Human Gene For Small Nuclear Rna U2 (Snrna U2)
Chain: 2

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Homo Sapiens U5 A Small Nuclear Rna
Chain: 5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Homo Sapiens Rna, U6 Small Nuclear 1 (Rnu6-1), Sm Nuclear Rna;
Chain: 6

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 5.90 Å
ligand MSE enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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

  • 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...
  • 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...
  • 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

  • catalytic step 2 spliceosome...
  • q

  • catalytic step 2 spliceosome...
  • Primary referenceCryo-EM structure of a human spliceosome activated for step 2 of splicing., Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R, Nature. 2017 Feb 16;542(7641):318-323. doi: 10.1038/nature21079. Epub 2017 Jan, 11. PMID:28076346
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1059 Kb) [Save to disk]
  • Biological Unit Coordinates (5mqf.pdb1.gz) 966 Kb
  • LPC: Ligand-Protein Contacts for 5MQF
  • CSU: Contacts of Structural Units for 5MQF
  • Retrieve 5MQF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MQF from S2C, [Save to disk]
  • View 5MQF 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 5MQF
  • 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 5mqf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mqf_L] [5mqf_J] [5mqf_D] [5mqf_X] [5mqf_a] [5mqf_i] [5mqf_H] [5mqf_Y] [5mqf_b] [5mqf_e] [5mqf] [5mqf_V] [5mqf_o] [5mqf_K] [5mqf_N] [5mqf_A] [5mqf_Q] [5mqf_T] [5mqf_G] [5mqf_P] [5mqf_2] [5mqf_n] [5mqf_f] [5mqf_p] [5mqf_R] [5mqf_g] [5mqf_E] [5mqf_I] [5mqf_h] [5mqf_F] [5mqf_d] [5mqf_k] [5mqf_S] [5mqf_M] [5mqf_j] [5mqf_Z] [5mqf_C] [5mqf_q] [5mqf_U] [5mqf_W] [5mqf_B] [5mqf_O] [5mqf_5] [5mqf_m] [5mqf_c] [5mqf_l] [5mqf_6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MQF
  • Community annotation for 5MQF at PDBWiki (http://pdbwiki.org)

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