6AH0 Splicing date Aug 15, 2018
title The Cryo-Em Structure Of The Precusor Of Human Pre-Catalytic Spliceosome (Pre-B Complex)
authors X.Zhan, C.Yan, X.Zhang, Y.Shi
compound source
Molecule: U5snrna
Chain: B
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U5 Small Nuclear Ribonucleoprotein 200 Kda Helica
Chain: D
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: U5 Small Nuclear Ribonucleoprotein 40 Kda Protein
Chain: E
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: Small Nuclear Ribonucleoprotein Sm D2
Chain: a, k, P
Synonym: Sm-D2,Snrnp Core Protein D2
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Small Nuclear Ribonucleoprotein F
Chain: b, m, Q
Synonym: Snrnp-F,Sm Protein F,Smf
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

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

Molecule: Small Nuclear Ribonucleoprotein G
Chain: d, n, S
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, h, T
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, I, U
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, j, V
Synonym: Sm-D1,Sm-D Autoantigen,Snrnp Core Protein D1
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6snrna
Chain: F
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm2
Chain: q
Synonym: Protein G7b,Small Nuclear Ribonuclear Protein D Ho Snrnp Core Sm-Like Protein Sm-X5;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm3
Chain: r
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm4
Chain: s
Synonym: Glycine-Rich Protein,Grp
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm5
Chain: t
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm6
Chain: x
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm7
Chain: y
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U6 Snrna-Associated Sm-Like Protein Lsm8
Chain: z
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2snrna
Chain: H
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2 Small Nuclear Ribonucleoprotein A'
Chain: o
Synonym: U2-A, U2 Snrnp A'
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U2 Small Nuclear Ribonucleoprotein B''
Chain: p
Synonym: U2 Snrnp B''
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3a Subunit 1
Chain: u
Synonym: Sf3a120,Spliceosome-Associated Protein 114,Sap 114
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3a Subunit 2
Chain: v
Synonym: Sf3a66,Spliceosome-Associated Protein 62,Sap 62
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3a Subunit 3
Chain: w
Synonym: Sf3a60,Spliceosome-Associated Protein 61,Sap 61
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 1
Chain: 1
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 2
Chain: 2
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: Splicing Factor 3b Subunit 3
Chain: 3
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 4
Chain: 4
Synonym: Pre-Mrna-Splicing Factor Sf3b 49 Kda Subunit,Splic Associated Protein 49,Sap 49;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Splicing Factor 3b Subunit 6
Chain: 5
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: Phd Finger-Like Domain-Containing Protein 5a
Chain: 6
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 5
Chain: 7
Synonym: Sf3b5,Pre-Mrna-Splicing Factor Sf3b 10 Kda Subunit
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp3
Chain: J
Synonym: Pre-Mrna-Splicing Factor 3,Hprp3,U4u6 Snrnp 90 Kd
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp4
Chain: K
Synonym: Prp4 Homolog,Hprp4,U4u6 Snrnp 60 Kda Protein,Wd S Factor Prp4;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Pre-Mrna-Processing Factor 6
Chain: N
Synonym: Androgen Receptor N-Terminal Domain-Transactivatin 1,Ant-1,Prp6 Homolog,U5 Snrnp-Associated 102 Kda Protein,U5 Protein;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6 Small Nuclear Ribonucleoprotein Prp31
Chain: L
Synonym: Pre-Mrna-Processing Factor 31,Serologically Define Cancer Antigen Ny-Br-99,U4u6 Snrnp 61 Kda Protein,Hprp31;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nhp2-Like Protein 1
Chain: M
Synonym: High Mobility Group-Like Nuclear Protein 2 Homolog Snu13 Homolog,Hsnu13,U4u6.U5 Small Nuclear Ribonucleoprote U4u6.U5 Tri-Snrnp 15.5 Kda Protein;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Thioredoxin-Like Protein 4a
Chain: O
Synonym: Dim1 Protein Homolog,Spliceosomal U5 Snrnp-Specifi Protein,Thioredoxin-Like U5 Snrnp Protein U5-15kd;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4u6.U5 Tri-Snrnp-Associated Protein 2
Chain: W
Synonym: Inactive Ubiquitin-Specific Peptidase 39,Sad1 Homo U4u6.U5 Tri-Snrnp-Associated 65 Kda Protein,65k;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: U4snrna
Chain: I
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Probable Atp-Dependent Rna Helicase Ddx23
Chain: X
Synonym: 100 Kda U5 Snrnp-Specific Protein,Dead Box Protein Homolog,U5-100kd;
Ec: 3.6.4.13
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: C
Synonym: Elongation Factor Tu Gtp-Binding Domain-Containing 2,Snu114 Homolog,Hsnu114,U5 Snrnp-Specific Protein,116 Kda,
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 5.70 Å
ligand GTP, IHP, MG enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1
  • splicing factor binding

  • catalytic step 2 spliceosome...
    • 2

  • spliceosomal complex
  • catalytic step 2 spliceosome...
    • 3
  • protein binding

  • catalytic step 2 spliceosome...
    • 4

  • spliceosomal complex
    • 5


    6


    7


    A
  • metallopeptidase activity
  • isopeptidase activity

  • catalytic step 2 spliceosome...
    • C


    D

  • U5 snRNP
  • catalytic step 2 spliceosome...
    • E

  • catalytic step 2 spliceosome...
    • J


    K

  • U4/U6 snRNP
    • L
  • spliceosomal tri-snRNP compl...
  • U4 snRNP
    • M


    N
  • spliceosomal tri-snRNP compl...
  • U4/U6 x U5 tri-snRNP complex...
  • catalytic step 2 spliceosome...
    • O


    S, d, n

  • catalytic step 2 spliceosome...
    • T, e, h

  • catalytic step 2 spliceosome...
    • U, f, i

  • catalytic step 2 spliceosome...
    • W


    X

  • U5 snRNP
  • catalytic step 2 spliceosome...
    • a, k, P

  • catalytic step 2 spliceosome...
    • b, Q, m

  • catalytic step 2 spliceosome...
    • c, l, R

  • catalytic step 2 spliceosome...
    • j, g, V

  • catalytic step 2 spliceosome...
    • o

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

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

  • catalytic step 2 spliceosome...
    • r

  • catalytic step 2 spliceosome...
    • s


    t


    u

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

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

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


    y


    z


    Primary referenceStructures of the human pre-catalytic spliceosome and its precursor spliceosome., Zhan X, Yan C, Zhang X, Lei J, Shi Y, Cell Res. 2018 Oct 12. pii: 10.1038/s41422-018-0094-7. doi:, 10.1038/s41422-018-0094-7. PMID:30315277
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1353 Kb) [Save to disk]
  • Biological Unit Coordinates (6ah0.pdb1.gz) 1250 Kb
  • LPC: Ligand-Protein Contacts for 6AH0
  • CSU: Contacts of Structural Units for 6AH0
  • Retrieve 6AH0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6AH0 from S2C, [Save to disk]
    • View 6AH0 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 6AH0
  • 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: [6ah0_z] [6ah0_3] [6ah0_q] [6ah0_p] [6ah0_h] [6ah0_K] [6ah0_j] [6ah0_r] [6ah0_U] [6ah0_N] [6ah0_T] [6ah0_l] [6ah0_y] [6ah0_e] [6ah0_V] [6ah0_A] [6ah0_n] [6ah0_s] [6ah0_t] [6ah0_Q] [6ah0_F] [6ah0_P] [6ah0_1] [6ah0_w] [6ah0_m] [6ah0_v] [6ah0_S] [6ah0_G] [6ah0_4] [6ah0_i] [6ah0_2] [6ah0_5] [6ah0_D] [6ah0_k] [6ah0_C] [6ah0_7] [6ah0_o] [6ah0_f] [6ah0_u] [6ah0_L] [6ah0_X] [6ah0_O] [6ah0_M] [6ah0_g] [6ah0_E] [6ah0_H] [6ah0_c] [6ah0_R] [6ah0_I] [6ah0_W] [6ah0_b] [6ah0_a] [6ah0_d] [6ah0_x] [6ah0_B] [6ah0_6] [6ah0_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6AH0
  • Community annotation for 6AH0 at PDBWiki (http://pdbwiki.org)

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