5MQF

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.9 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

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

  • 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 Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8 (PRPC8)
Find proteins for Q6P2Q9 (Homo sapiens)
Go to Gene View: PRPF8
Go to UniProtKB:  Q6P2Q9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
B
972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2 (KIAA0031, SNRP116)
Find proteins for Q15029 (Homo sapiens)
Go to Gene View: EFTUD2
Go to UniProtKB:  Q15029
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SNW domain-containing protein 1
C
536Homo sapiensMutation(s): 0 
Gene Names: SNW1 (SKIIP, SKIP)
Find proteins for Q13573 (Homo sapiens)
Go to Gene View: SNW1
Go to UniProtKB:  Q13573
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pleiotropic regulator 1
D
515Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
Go to Gene View: PLRG1
Go to UniProtKB:  O43660
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
E
579Homo sapiensMutation(s): 0 
Gene Names: CDC40 (EHB3, PRP17, PRPF17)
Find proteins for O60508 (Homo sapiens)
Go to Gene View: CDC40
Go to UniProtKB:  O60508
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
F
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40 (PRP8BP, SFP38, WDR57)
Find proteins for Q96DI7 (Homo sapiens)
Go to Gene View: SNRNP40
Go to UniProtKB:  Q96DI7
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
G, H, I, J
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19 (NMP200, PRP19, SNEV)
EC: 2.3.2.27
Find proteins for Q9UMS4 (Homo sapiens)
Go to Gene View: PRPF19
Go to UniProtKB:  Q9UMS4
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPF27
K
225Homo sapiensMutation(s): 0 
Gene Names: BCAS2 (DAM1)
Find proteins for O75934 (Homo sapiens)
Go to Gene View: BCAS2
Go to UniProtKB:  O75934
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle 5-like protein
L
802Homo sapiensMutation(s): 0 
Gene Names: CDC5L (KIAA0432, PCDC5RP)
Find proteins for Q99459 (Homo sapiens)
Go to Gene View: CDC5L
Go to UniProtKB:  Q99459
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
M
855Homo sapiensMutation(s): 0 
Gene Names: XAB2 (HCNP, KIAA1177, SYF1)
Find proteins for Q9HCS7 (Homo sapiens)
Go to Gene View: XAB2
Go to UniProtKB:  Q9HCS7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
N
243Homo sapiensMutation(s): 0 
Gene Names: SYF2 (CBPIN, GCIPIP)
Find proteins for O95926 (Homo sapiens)
Go to Gene View: SYF2
Go to UniProtKB:  O95926
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Crooked neck-like protein 1
O
848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1 (CRN)
Find proteins for Q9BZJ0 (Homo sapiens)
Go to Gene View: CRNKL1
Go to UniProtKB:  Q9BZJ0
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RBM22
P
420Homo sapiensMutation(s): 0 
Gene Names: RBM22 (ZC3H16)
Find proteins for Q9NW64 (Homo sapiens)
Go to Gene View: RBM22
Go to UniProtKB:  Q9NW64
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Protein BUD31 homolog
Q
144Homo sapiensMutation(s): 0 
Gene Names: BUD31 (EDG2)
Find proteins for P41223 (Homo sapiens)
Go to Gene View: BUD31
Go to UniProtKB:  P41223
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Spliceosome-associated protein CWC15 homolog
R
229Homo sapiensMutation(s): 0 
Gene Names: CWC15 (C11orf5)
Find proteins for Q9P013 (Homo sapiens)
Go to Gene View: CWC15
Go to UniProtKB:  Q9P013
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Serine/arginine repetitive matrix protein 2
S
2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2 (KIAA0324, SRL300, SRM300)
Find proteins for Q9UQ35 (Homo sapiens)
Go to Gene View: SRRM2
Go to UniProtKB:  Q9UQ35
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22 homolog
T
908Homo sapiensMutation(s): 0 
Gene Names: CWC22 (KIAA1604, NCM)
Find proteins for Q9HCG8 (Homo sapiens)
Go to Gene View: CWC22
Go to UniProtKB:  Q9HCG8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Intron-binding protein aquarius
U
1485Homo sapiensMutation(s): 0 
Gene Names: AQR (KIAA0560)
EC: 3.6.4.13
Find proteins for O60306 (Homo sapiens)
Go to Gene View: AQR
Go to UniProtKB:  O60306
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase-like 1
V
166Homo sapiensMutation(s): 0 
Gene Names: PPIL1 (CYPL1)
EC: 5.2.1.8
Find proteins for Q9Y3C6 (Homo sapiens)
Go to Gene View: PPIL1
Go to UniProtKB:  Q9Y3C6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
Go to Gene View: SNRPA1
Go to UniProtKB:  P09661
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
X
225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
Go to Gene View: SNRPB2
Go to UniProtKB:  P08579
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
a, h
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2 (SNRPD1)
Find proteins for P62316 (Homo sapiens)
Go to Gene View: SNRPD2
Go to UniProtKB:  P62316
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
b, i
86Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
c, j
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
d, k
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
e, l
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
f, m
240Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
g, n
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase E
o
301Homo sapiensMutation(s): 0 
Gene Names: PPIE (CYP33)
EC: 5.2.1.8
Find proteins for Q9UNP9 (Homo sapiens)
Go to Gene View: PPIE
Go to UniProtKB:  Q9UNP9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic initiation factor 4A-III
p
411Homo sapiensMutation(s): 0 
Gene Names: EIF4A3 (DDX48, KIAA0111)
EC: 3.6.4.13
Find proteins for P38919 (Homo sapiens)
Go to Gene View: EIF4A3
Go to UniProtKB:  P38919
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DHX8
q
1218Homo sapiensMutation(s): 0 
Gene Names: DHX8 (DDX8)
EC: 3.6.4.13
Find proteins for Q14562 (Homo sapiens)
Go to Gene View: DHX8
Go to UniProtKB:  Q14562
Entity ID: 32
MoleculeChainsLengthOrganism
MINX pre-mRNA (intron)Y,Z324Homo sapiens
Entity ID: 33
MoleculeChainsLengthOrganism
Human gene for small nuclear RNA U2 (snRNA U2)2188Homo sapiens
Entity ID: 34
MoleculeChainsLengthOrganism
Homo sapiens U5 A small nuclear RNA5116Homo sapiens
Entity ID: 35
MoleculeChainsLengthOrganism
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
U
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Author supporting evidence