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: 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 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

    Department for Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: hstark1@gwdg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2A [auth 1]322Homo sapiensMutation(s): 0 
Gene Names: RBMX2CGI-79
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homologC [auth 3]619Homo sapiensMutation(s): 0 
Gene Names: BUD13
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2F [auth 7]464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2G [auth 8]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8H [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentI [auth B]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 10
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SNW domain-containing protein 1J [auth C]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 11
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Pleiotropic regulator 1K [auth D]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 12
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Pre-mRNA-processing factor 17L [auth E]579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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Entity ID: 13
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Cell division cycle 5-like proteinM [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Crooked neck-like protein 1N [auth O]848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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Entity ID: 15
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Pre-mRNA-splicing factor RBM22O [auth P]420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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Entity ID: 16
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Protein BUD31 homologP [auth Q]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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Entity ID: 17
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Spliceosome-associated protein CWC15 homologQ [auth R]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 18
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Serine/arginine repetitive matrix protein 2R [auth S]2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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Entity ID: 19
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Peptidyl-prolyl cis-trans isomerase-like 1S [auth V]166Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
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Entity ID: 20
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Serine/arginine repetitive matrix protein 1T [auth Y]904Homo sapiensMutation(s): 0 
Gene Names: SRRM1SRM160
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Entity ID: 22
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Peptidyl-prolyl cis-trans isomerase CWC27 homologV [auth s]472Homo sapiensMutation(s): 0 
Gene Names: CWC27SDCCAG10UNQ438/PRO871
EC: 5.2.1.8
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Entity ID: 23
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RING finger protein 113AW [auth t]343Homo sapiensMutation(s): 0 
Gene Names: RNF113ARNF113ZNF183
EC: 2.3.2.27
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Entity ID: 24
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Splicing factor 3B subunit 1X [auth u]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 25
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Splicing factor 3B subunit 3Y [auth v]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 26
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Splicing factor 3B subunit 5Z [auth x]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 27
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PHD finger-like domain-containing protein 5AAA [auth y]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6IB [auth N], BA [auth z]125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
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Entity ID: 29
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Smad nuclear-interacting protein 1CA [auth 0]396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3DA [auth 9]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinEA [auth F]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19FA [auth G], GA [auth H], HA [auth I], IA [auth J]504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
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Entity ID: 33
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Pre-mRNA-splicing factor SPF27JA [auth K]225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
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Entity ID: 34
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Pre-mRNA-splicing factor SYF1KA [auth M]855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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Entity ID: 35
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Pre-mRNA-splicing factor CWC22 homologLA [auth T]908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
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Entity ID: 36
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Intron-binding protein aquariusMA [auth U]1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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Entity ID: 37
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U2 small nuclear ribonucleoprotein A'NA [auth W]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 38
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U2 small nuclear ribonucleoprotein B''OA [auth X]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 39
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Small nuclear ribonucleoprotein Sm D2PA [auth a], WA [auth h]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 40
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Small nuclear ribonucleoprotein FQA [auth b], XA [auth i]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 41
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Small nuclear ribonucleoprotein ERA [auth c], YA [auth j]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 42
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Small nuclear ribonucleoprotein GSA [auth d], ZA [auth k]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 43
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Small nuclear ribonucleoprotein Sm D3TA [auth e], AB [auth l]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 44
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Small nuclear ribonucleoprotein-associated proteins B and B'UA [auth f], BB [auth m]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 45
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Small nuclear ribonucleoprotein Sm D1VA [auth g], CB [auth n]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 46
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Peptidyl-prolyl cis-trans isomerase EDB [auth o]301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
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Entity ID: 47
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Splicing factor 3A subunit 1EB [auth p]793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
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Entity ID: 48
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Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16FB [auth q]1041Homo sapiensMutation(s): 0 
Gene Names: DHX16DBP2DDX16KIAA0577PRP2
EC: 3.6.4.13
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Entity ID: 49
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U5 small nuclear ribonucleoprotein 200 kDa helicaseGB [auth r]2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 50
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Pre-mRNA-splicing factor ISY1 homologHB [auth w]285Homo sapiensMutation(s): 0 
Gene Names: ISY1KIAA1160
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Entity ID: 2
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U2 snRNAB [auth 2]188Homo sapiens
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Entity ID: 4
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U5 snRNAD [auth 5]116Homo sapiens
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Entity ID: 5
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U6 snRNAE [auth 6]107Homo sapiens
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Entity ID: 21
MoleculeChainsLengthOrganismImage
pre-mRNAU [auth Z]369Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
GTP
Query on GTP

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

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JB [auth 2] , QB [auth P] , RB [auth P] , SB [auth P] , TB [auth Q] , UB [auth Q] , VB [auth Q] , WB [auth Z] , 
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
 Ligand Interaction
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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