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 ( ...

    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
Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS  Q6P2Q9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentB972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1C536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
Find proteins for Q13573 (Homo sapiens)
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PHAROS  Q13573
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1D515Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
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PHAROS  O43660
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17E579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
Find proteins for O60508 (Homo sapiens)
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PHAROS  O60508
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinF357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
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PHAROS  Q96DI7
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19GHIJ504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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PHAROS  Q9UMS4
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27K225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
Find proteins for O75934 (Homo sapiens)
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PHAROS  O75934
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
Find proteins for Q99459 (Homo sapiens)
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PHAROS  Q99459
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1M855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
Find proteins for Q9HCS7 (Homo sapiens)
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PHAROS  Q9HCS7
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2N243Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
Find proteins for O95926 (Homo sapiens)
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PHAROS  O95926
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1O848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
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PHAROS  Q9BZJ0
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22P420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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PHAROS  Q9NW64
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologQ144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
Find proteins for P41223 (Homo sapiens)
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PHAROS  P41223
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologR229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
Find proteins for Q9P013 (Homo sapiens)
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PHAROS  Q9P013
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2S2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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PHAROS  Q9UQ35
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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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PHAROS  Q9HCG8
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-binding protein aquariusU1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
Find proteins for O60306 (Homo sapiens)
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PHAROS  O60306
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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
Find proteins for Q9Y3C6 (Homo sapiens)
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PHAROS  Q9Y3C6
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'W255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
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PHAROS  P09661
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''X225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
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PHAROS  P08579
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2ah118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
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PHAROS  P62316
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Fbi86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ecj92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Gdk76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3el126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'fm240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1gn119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase Eo301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
Find proteins for Q9UNP9 (Homo sapiens)
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PHAROS  Q9UNP9
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIp411Homo sapiensMutation(s): 0 
Gene Names: EIF4A3DDX48KIAA0111
EC: 3.6.4.13
Find proteins for P38919 (Homo sapiens)
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PHAROS  P38919
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8q1218Homo sapiensMutation(s): 0 
Gene Names: DHX8DDX8
EC: 3.6.4.13
Find proteins for Q14562 (Homo sapiens)
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PHAROS  Q14562
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Entity ID: 32
MoleculeChainsLengthOrganismImage
MINX pre-mRNA (intron)Y, Z324Homo sapiens
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Entity ID: 33
MoleculeChainsLengthOrganismImage
Human gene for small nuclear RNA U2 (snRNA U2)2188Homo sapiens
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Entity ID: 34
MoleculeChainsLengthOrganismImage
Homo sapiens U5 A small nuclear RNA5116Homo sapiens
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Entity ID: 35
MoleculeChainsLengthOrganismImage
Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA6106Homo sapiens
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 

  • 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