7A5P Splicing date Aug 21, 2020
title Human C Complex Spliceosome - Medium-Resolution Periphery
authors K.Bertram, B.Kastner
compound source
Molecule: U2 Snrna
Chain: 2
 Organism_scientific: Homo Sapiens
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_taxid: 9606
Strain: Hela S3

Molecule: Unknown
Chain: 8
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Strain: 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

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: 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: 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: 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: 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
Ec: 3.6.4.13
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: Pre-Mrna
Chain: Y
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Strain: Hela S3

Molecule: Small Nuclear Ribonucleoprotein Sm D3
Chain: a, 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: b, 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: c, n
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, h
Synonym: Sm-D2,Snrnp Core Protein D2
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein E
Chain: e, j
Synonym: Snrnp-E,Sm Protein E,Sme
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein F
Chain: f, I
Synonym: Snrnp-F,Sm Protein F,Smf
Other_details: Mslplnpkpflngltgkpvmvklkwgmeykgylvsvdgymnmqlanteeyidgalsghl Lyirgveeeeedgemre;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein G
Chain: g, k
Synonym: Snrnp-G,Sm Protein G,Smg
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: Wd Repeat-Containing Protein 70
Chain: p
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5 Small Nuclear Ribonucleoprotein 200 Kda Helica
Chain: q
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 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: Splicing Factor Yju2
Chain: u
Synonym: Coiled-Coil Domain-Containing Protein 94
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein Mago Nashi Homolog
Chain: v
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Rna-Binding Protein 8a
Chain: w
Synonym: Binder Of Ovca1-1,Bov-1,Rna-Binding Motif Protein Binding Protein Y14,Ribonucleoprotein Rbm8a;
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

Molecule: Eukaryotic Initiation Factor 4a-III
Chain: y
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: Peptidylprolyl Isomerase Domain And Wd Repeat-Con Protein 1;
Chain: z
Synonym: Spliceosome-Associated Cyclophilin
Ec: 5.2.1.8
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 5.00 Å
ligand MSE enzyme Transferase E.C.2.3.2.27 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] (1156 Kb) [Save to disk]
  • Biological Unit Coordinates (7a5p.pdb1.gz) 1023 Kb
  • LPC: Ligand-Protein Contacts for 7A5P
  • CSU: Contacts of Structural Units for 7A5P
  • Retrieve 7A5P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 7A5P from S2C, [Save to disk]
    • View 7A5P 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 7A5P
  • 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: [7a5p_z] [7a5p_c] [7a5p_v] [7a5p_K] [7a5p_H] [7a5p_5] [7a5p_l] [7a5p_N] [7a5p_2] [7a5p_i] [7a5p_O] [7a5p_u] [7a5p_U] [7a5p_L] [7a5p_G] [7a5p_M] [7a5p_d] [7a5p_P] [7a5p_p] [7a5p_I] [7a5p_y] [7a5p_W] [7a5p_f] [7a5p_6] [7a5p_n] [7a5p_E] [7a5p_h] [7a5p_J] [7a5p_C] [7a5p_e] [7a5p_8] [7a5p_m] [7a5p_o] [7a5p_s] [7a5p_A] [7a5p_k] [7a5p_r] [7a5p_a] [7a5p_S] [7a5p_j] [7a5p_w] [7a5p_b] [7a5p_g] [7a5p_Y] [7a5p_T] [7a5p_X] [7a5p_x] [7a5p_q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 7A5P
  • Community annotation for 7A5P at PDBWiki (http://pdbwiki.org)

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