5MQF

Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 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

Cryo-EM structure of a human spliceosome activated for step 2 of splicing.

Bertram, K.Agafonov, D.E.Liu, W.T.Dybkov, O.Will, C.L.Hartmuth, K.Urlaub, H.Kastner, B.Stark, H.Lu Hrmann, R.

(2017) Nature 542: 318-323

  • DOI: 10.1038/nature21079
  • Primary Citation of Related Structures:  
    5MQF

  • PubMed Abstract: 
  • Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex ...

    Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C* spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated from the catalytic centre by approximately 20 Å, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 Å from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C* complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP.


    Organizational Affiliation

    Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentB972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1C536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1D515Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17E579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinF357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19G, H, I, J504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27K225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1M855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2N243Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1O848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22P420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologQ144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologR229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 16
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Serine/arginine repetitive matrix protein 2S2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologT908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-binding protein aquariusU1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1V166Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'W255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''X225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2Y [auth a], FA [auth h]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FZ [auth b], GA [auth i]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EAA [auth c], HA [auth j]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GBA [auth d], IA [auth k]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3CA [auth e], JA [auth l]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'DA [auth f], KA [auth m]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1EA [auth g], LA [auth n]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EMA [auth o]301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIINA [auth p]411Homo sapiensMutation(s): 0 
Gene Names: EIF4A3DDX48KIAA0111
EC: 3.6.4.13
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8OA [auth q]1218Homo sapiensMutation(s): 0 
Gene Names: DHX8DDX8
EC: 3.6.4.13
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Entity ID: 32
MoleculeChainsLengthOrganismImage
MINX pre-mRNA (intron)PA [auth Y], QA [auth Z]324Homo sapiens
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Entity ID: 33
MoleculeChainsLengthOrganismImage
Human gene for small nuclear RNA U2 (snRNA U2)RA [auth 2]188Homo sapiens
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Entity ID: 34
MoleculeChainsLengthOrganismImage
Homo sapiens U5 A small nuclear RNASA [auth 5]116Homo sapiens
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Entity ID: 35
MoleculeChainsLengthOrganismImage
Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNATA [auth 6]106Homo sapiens
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
UL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 860

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations