6AH0

The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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

Structures of the human pre-catalytic spliceosome and its precursor spliceosome.

Zhan, X.Yan, C.Zhang, X.Lei, J.Shi, Y.

(2018) Cell Res 28: 1129-1140

  • DOI: 10.1038/s41422-018-0094-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B act complex). The pre-B-to-B and B-to-B act transitions are driven by the ATPase/h ...

    The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B act complex). The pre-B-to-B and B-to-B act transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.


    Organizational Affiliation

    Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang, 310024, China. shi-lab@tsinghua.edu.cn.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 200 kDa helicase
D
2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
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PHAROS  O75643

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
E
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
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PHAROS  Q96DI7

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
P, a, k
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
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PHAROS  P62316

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
Q, b, m
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
R, c, l
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
T, e, h
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
V, g, j
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
q
95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
Find proteins for Q9Y333 (Homo sapiens)
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PHAROS  Q9Y333

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
r
102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
Find proteins for P62310 (Homo sapiens)
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PHAROS  P62310

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
s
139Homo sapiensMutation(s): 0 
Gene Names: LSM4
Find proteins for Q9Y4Z0 (Homo sapiens)
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PHAROS  Q9Y4Z0

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
t
91Homo sapiensMutation(s): 0 
Gene Names: LSM5
Find proteins for Q9Y4Y9 (Homo sapiens)
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PHAROS  Q9Y4Y9

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
y
103Homo sapiensMutation(s): 0 
Gene Names: LSM7
Find proteins for Q9UK45 (Homo sapiens)
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PHAROS  Q9UK45

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
o
255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
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PHAROS  P09661

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
p
225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
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PHAROS  P08579

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 1
u
793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
Find proteins for Q15459 (Homo sapiens)
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PHAROS  Q15459

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 2
v
464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
Find proteins for Q15428 (Homo sapiens)
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PHAROS  Q15428

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 3
w
501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
Find proteins for Q12874 (Homo sapiens)
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PHAROS  Q12874

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 1
1
1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
Find proteins for O75533 (Homo sapiens)
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PHAROS  O75533

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 2
2
895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
Find proteins for Q13435 (Homo sapiens)
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PHAROS  Q13435

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 3
3
1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
Find proteins for Q15393 (Homo sapiens)
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PHAROS  Q15393

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 4
4
424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
Find proteins for Q15427 (Homo sapiens)
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PHAROS  Q15427

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 6
5
125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
Find proteins for Q9Y3B4 (Homo sapiens)
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PHAROS  Q9Y3B4

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
PHD finger-like domain-containing protein 5A
6
110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
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PHAROS  Q7RTV0

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 5
7
86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
Find proteins for Q9BWJ5 (Homo sapiens)
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PHAROS  Q9BWJ5

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp4
K
522Homo sapiensMutation(s): 0 
Gene Names: PRPF4PRP4
Find proteins for O43172 (Homo sapiens)
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PHAROS  O43172

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 6
N
941Homo sapiensMutation(s): 0 
Gene Names: PRPF6C20orf14
Find proteins for O94906 (Homo sapiens)
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PHAROS  O94906

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp31
L
499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
Find proteins for Q8WWY3 (Homo sapiens)
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PHAROS  Q8WWY3

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
NHP2-like protein 1
M
128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
Find proteins for P55769 (Homo sapiens)
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PHAROS  P55769

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin-like protein 4A
O
142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
Find proteins for P83876 (Homo sapiens)
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PHAROS  P83876

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
U4/U6.U5 tri-snRNP-associated protein 2
W
565Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
Find proteins for Q53GS9 (Homo sapiens)
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PHAROS  Q53GS9

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent RNA helicase DDX23
X
820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
Find proteins for Q9BUQ8 (Homo sapiens)
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PHAROS  Q9BUQ8

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS  Q6P2Q9

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
C
972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
x
80Homo sapiensMutation(s): 0 
Gene Names: LSM6
Find proteins for P62312 (Homo sapiens)
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PHAROS  P62312

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
z
96Homo sapiensMutation(s): 0 
Gene Names: LSM8
Find proteins for O95777 (Homo sapiens)
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PHAROS  O95777

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein Prp3
J
683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
Find proteins for O43395 (Homo sapiens)
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PHAROS  O43395

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
S, d, n
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
U, f, i
231Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678

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Entity ID: 1
MoleculeChainsLengthOrganism
U5snRNAB117Homo sapiens

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Entity ID: 11
MoleculeChainsLengthOrganism
U6snRNAF107Homo sapiens

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Entity ID: 19
MoleculeChainsLengthOrganism
pre-mRNAG274Homo sapiens

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Entity ID: 20
MoleculeChainsLengthOrganism
U2snRNAH188Homo sapiens

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Entity ID: 40
MoleculeChainsLengthOrganism
U4snRNAI144Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download CCD File 
A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

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C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31430020

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references