7ABG

Human pre-Bact-1 spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.

Townsend, C.Leelaram, M.N.Agafonov, D.E.Dybkov, O.Will, C.L.Bertram, K.Urlaub, H.Kastner, B.Stark, H.Luhrmann, R.

(2020) Science 370

  • DOI: 10.1126/science.abc3753
  • Primary Citation of Related Structures:  
    7AAV, 7ABI, 7ABH, 7ABG, 7ABF

  • PubMed Abstract: 
  • Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding ...

    Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B act complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B act complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.


    Organizational Affiliation

    Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. reinhard.luehrmann@mpibpc.mpg.de hstark1@gwdg.de b.kastner@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 1A [auth A5]790Homo sapiensMutation(s): 0 
Gene Names: NCBP1CBP80NCBP
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7B [auth A2]103Homo sapiensMutation(s): 0 
Gene Names: LSM7
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Find proteins for Q9UK45 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6C [auth z]125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2D [auth F]464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinE [auth D]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'F [auth W]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''G [auth B]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseH [auth s]2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologI [auth Q]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 2J [auth A1]156Homo sapiensMutation(s): 0 
Gene Names: NCBP2CBP20PIG55
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologM [auth R]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2N [auth V]95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3O [auth 9]102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4P [auth C]139Homo sapiensMutation(s): 0 
Gene Names: LSM4
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5Q [auth H]91Homo sapiensMutation(s): 0 
Gene Names: LSM5
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6R [auth J]80Homo sapiensMutation(s): 0 
Gene Names: LSM6
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8T [auth A3]96Homo sapiensMutation(s): 0 
Gene Names: LSM8
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1U [auth K]439Homo sapiensMutation(s): 0 
Gene Names: MFAP1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AV [auth y]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1W [auth G]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8Y [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AZ [auth I]312Homo sapiensMutation(s): 0 
Gene Names: PRPF38A
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22AA [auth P]420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1BA [auth p]793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3CA [auth 4]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation regulator 1DA [auth A4]1098Homo sapiensMutation(s): 0 
Gene Names: TCERG1CA150TAF2S
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1EA [auth u]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2FA [auth T]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3GA [auth E]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4HA [auth w]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5IA [auth x]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1JA [auth v]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1KA [auth 0]396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2LA [auth N]199Homo sapiensMutation(s): 0 
Gene Names: ZMAT2
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentMA [auth r]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1NA [auth Y]904Homo sapiensMutation(s): 0 
Gene Names: SRRM1SRM160
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine-rich splicing factor 1PA [auth A6]248Homo sapiensMutation(s): 0 
Gene Names: SRSF1ASFSF2SF2P33SFRS1OK/SW-cl.3
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2ZA [auth a], QA [auth h]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FCB [auth b], RA [auth i]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'XA [auth f], SA [auth m]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3AB [auth e], TA [auth l]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Find proteins for P62318 (Homo sapiens)
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GDB [auth d], UA [auth k]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBB [auth c], VA [auth j]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1YA [auth g], WA [auth n]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 50
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Ubiquitin-like protein 5EB [auth q]73Homo sapiensMutation(s): 0 
Gene Names: UBL5
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Find proteins for Q9BZL1 (Homo sapiens)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
WW domain-binding protein 11FB [auth X]641Homo sapiensMutation(s): 0 
Gene Names: WBP11NPWBPSIPP1SNP70
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Entity ID: 11
MoleculeChainsLengthOrganismImage
U5 snRNAK [auth 5]116Homo sapiens
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Entity ID: 19
MoleculeChainsLengthOrganismImage
U2 snRNAS [auth 2]188Homo sapiens
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Entity ID: 24
MoleculeChainsLengthOrganismImage
MINX M3 pre-mRNAX [auth Z]230synthetic construct
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Entity ID: 41
MoleculeChainsLengthOrganismImage
U6 snRNAOA [auth 6]106Homo sapiens
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTG (Subject of Investigation/LOI)
Query on GTG

Download Ideal Coordinates CCD File 
JB [auth A6]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
 Ligand Interaction
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
GB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
HB [auth r]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
IB [auth r]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany860

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references