5Z56

cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the human activated spliceosome in three conformational states.

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

(2018) Cell Res 28: 307-322

  • DOI: 10.1038/cr.2018.14
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B act complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we pres ...

    During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B act complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B act complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B act complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B act complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B act and the B act -to-B * transitions, which ultimately prime the active site for the branching reaction.


    Organizational Affiliation

    Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Shilongshan Road No. 18, Hangzhou, Zhejiang 310064, China.



Macromolecules

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Entity ID: 1
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: 3
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: 4
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: 5
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: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
a, 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: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
b, 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: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
c, 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: 9
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
d, 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: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, 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: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, 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: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, 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: 16
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: 17
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: 18
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: 19
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: 20
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: 21
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: 22
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: 23
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: 24
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: 25
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: 26
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: 27
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: 28
MoleculeChainsSequence LengthOrganismDetails
Crooked neck-like protein 1
J
848Homo 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: 29
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle 5-like protein
L
802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
Find proteins for Q99459 (Homo sapiens)
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PHAROS  Q99459
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
q, r, s, t
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
Find proteins for Q9UMS4 (Homo sapiens)
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PHAROS  Q9UMS4
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPF27
K
225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
Find proteins for O75934 (Homo sapiens)
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PHAROS  O75934
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
I
855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
Find proteins for Q9HCS7 (Homo sapiens)
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PHAROS  Q9HCS7
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Intron-binding protein aquarius
Q
1485Homo 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: 34
MoleculeChainsSequence LengthOrganismDetails
RING finger protein 113A
M
343Homo sapiensMutation(s): 0 
Gene Names: RNF113ARNF113ZNF183
EC: 2.3.2.27
Find proteins for O15541 (Homo sapiens)
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PHAROS  O15541
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Protein BUD31 homolog
N
144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
Find proteins for P41223 (Homo sapiens)
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PHAROS  P41223
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RBM22
O
420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
Find proteins for Q9NW64 (Homo sapiens)
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PHAROS  Q9NW64
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Spliceosome-associated protein CWC15 homolog
P
229Homo 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: 38
MoleculeChainsSequence LengthOrganismDetails
Skip
R
540Homo sapiensMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase-like 1
S
166Homo 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: 40
MoleculeChainsSequence LengthOrganismDetails
Pleiotropic regulator 1
T
514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
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PHAROS  O43660
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Serine/arginine repetitive matrix protein 2
U
2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
Find proteins for Q9UQ35 (Homo sapiens)
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PHAROS  Q9UQ35
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22 homolog
V
908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
Find proteins for Q9HCG8 (Homo sapiens)
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PHAROS  Q9HCG8
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
W
579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
Find proteins for O60508 (Homo sapiens)
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PHAROS  O60508
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Smad nuclear-interacting protein 1
X
396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
Find proteins for Q8TAD8 (Homo sapiens)
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PHAROS  Q8TAD8
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
RNA-binding motif protein, X-linked 2
Y
322Homo sapiensMutation(s): 0 
Gene Names: RBMX2CGI-79
Find proteins for Q9Y388 (Homo sapiens)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
BUD13 homolog
Z
619Homo sapiensMutation(s): 0 
Gene Names: BUD13
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PHAROS  Q9BRD0
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase CWC27 homolog
z
472Homo sapiensMutation(s): 0 
Gene Names: CWC27SDCCAG10UNQ438/PRO871
EC: 5.2.1.8
Find proteins for Q6UX04 (Homo sapiens)
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PHAROS  Q6UX04
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
x
1041Homo sapiensMutation(s): 0 
Gene Names: DHX16DBP2DDX16KIAA0577PRP2
EC: 3.6.4.13
Find proteins for O60231 (Homo sapiens)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase E
y
301Homo 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: 2
MoleculeChainsLengthOrganism
U5 snRNAB117Homo sapiens

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Entity ID: 13
MoleculeChainsLengthOrganism
U6 snRNAF107Homo sapiens

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Entity ID: 14
MoleculeChainsLengthOrganism
pre-mRNAG274unidentified adenovirus

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Entity ID: 15
MoleculeChainsLengthOrganism
U2 snRNAH188Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

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A
INOSITOL 1,2,3,4,5,6-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
ZN
Query on ZN

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6, M, N, O, W, v
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31430020
Ministry of Science and Technology (China)China2016YFA0501100

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other