6FF7

human Bact spliceosome core structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and Conformational Dynamics of the Human Spliceosomal BactComplex.

Haselbach, D.Komarov, I.Agafonov, D.E.Hartmuth, K.Graf, B.Dybkov, O.Urlaub, H.Kastner, B.Luhrmann, R.Stark, H.

(2018) Cell 172: 454-464.e11

  • DOI: https://doi.org/10.1016/j.cell.2018.01.010
  • Primary Citation of Related Structures:  
    6FF4, 6FF7

  • PubMed Abstract: 

    The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B act spliceosome at 3.4 Å resolution. In the B act state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B act spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.


  • Organizational Affiliation

    Bioanalytic Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Str. 40, 37073 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2A [auth 1]322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134597 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BUD13 homologC [auth 3]619Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137656 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2F [auth 7]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2G [auth 8]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8H [auth A]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentI [auth B]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1J [auth C]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1K [auth D]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17L [auth E]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinM [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1N [auth O]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22O [auth P]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologP [auth Q]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologQ [auth R]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2R [auth S]2,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1S [auth V]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1T [auth Y]904Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133226 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologV [auth s]472Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000153015 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RING finger protein 113AW [auth t]343Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125352 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1X [auth u]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3Y [auth v]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5Z [auth x]86Homo sapiensMutation(s): 0 
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PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AAA [auth y]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6BA [auth z],
IB [auth N]
125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115128 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1CA [auth 0]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163877 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3DA [auth 9]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinEA [auth F]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19FA [auth G],
GA [auth H],
HA [auth I],
IA [auth J]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27JA [auth K]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1KA [auth M]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologLA [auth T]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusMA [auth U]1,485Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000021776 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'NA [auth W]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''OA [auth X]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2PA [auth a],
WA [auth h]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FQA [auth b],
XA [auth i]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ERA [auth c],
YA [auth j]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GSA [auth d],
ZA [auth k]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3AB [auth l],
TA [auth e]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'BB [auth m],
UA [auth f]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1CB [auth n],
VA [auth g]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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UniProt GroupP62314
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EDB [auth o]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9UNP9 (Homo sapiens)
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GTEx:  ENSG00000084072 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1EB [auth p]793Homo sapiensMutation(s): 0 
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Find proteins for Q15459 (Homo sapiens)
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GTEx:  ENSG00000099995 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16FB [auth q]1,041Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O60231 (Homo sapiens)
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GTEx:  ENSG00000204560 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseGB [auth r]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O75643 (Homo sapiens)
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GTEx:  ENSG00000144028 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologHB [auth w]285Homo sapiensMutation(s): 0 
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Find proteins for Q9ULR0 (Homo sapiens)
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GTEx:  ENSG00000240682 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U2 snRNAB [auth 2]188Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
U5 snRNAD [auth 5]116Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
U6 snRNAE [auth 6]107Homo sapiens
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Entity ID: 21
MoleculeChains LengthOrganismImage
pre-mRNAU [auth Z]369Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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OB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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PB [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ADP
Query on ADP

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AC [auth r],
BC [auth r]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

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JB [auth 2]
QB [auth P]
RB [auth P]
SB [auth P]
TB [auth Q]
JB [auth 2],
QB [auth P],
RB [auth P],
SB [auth P],
TB [auth Q],
UB [auth Q],
VB [auth Q],
WB [auth Z],
XB [auth y],
YB [auth y],
ZB [auth y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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CC [auth r],
KB [auth 6],
LB [auth 6],
MB [auth 6],
NB [auth 6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-12-11
    Changes: Other
  • Version 1.3: 2020-10-07
    Changes: Derived calculations, Structure summary