+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The cryo-EM map of the human 17S U2 snRNP core region | |||||||||
![]() | The EM map of U2 snRNP | |||||||||
![]() |
| |||||||||
![]() | U2 snRNP / PRP5 / ![]() ![]() | |||||||||
Function / homology | ![]() U11/U12 snRNP / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhang X / Zhan X | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural insights into branch site proofreading by human spliceosome. Authors: Xiaofeng Zhang / Xiechao Zhan / Tong Bian / Fenghua Yang / Pan Li / Yichen Lu / Zhihan Xing / Rongyan Fan / Qiangfeng Cliff Zhang / Yigong Shi / ![]() Abstract: Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the ...Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 116.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 36.4 KB 36.4 KB | Display Display | ![]() |
Images | ![]() | 35.5 KB | ||
Filedesc metadata | ![]() | 12.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7evoMC ![]() 7vpxC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The EM map of U2 snRNP | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
+Entire : The human U2 snRNP
+Supramolecule #1: The human U2 snRNP
+Macromolecule #1: U2 snRNA
+Macromolecule #2: Splicing factor 3B subunit 1
+Macromolecule #3: Splicing factor 3B subunit 2
+Macromolecule #4: Splicing factor 3B subunit 3
+Macromolecule #5: Splicing factor 3B subunit 4
+Macromolecule #6: Splicing factor 3B subunit 5
+Macromolecule #7: PHD finger-like domain-containing protein 5A
+Macromolecule #8: Splicing factor 3A subunit 1
+Macromolecule #9: Splicing factor 3A subunit 2
+Macromolecule #10: Splicing factor 3A subunit 3
+Macromolecule #11: HIV Tat-specific factor 1
+Macromolecule #12: RNA helicase
+Macromolecule #13: U2 small nuclear ribonucleoprotein A'
+Macromolecule #14: U2 small nuclear ribonucleoprotein B''
+Macromolecule #15: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #16: Small nuclear ribonucleoprotein F
+Macromolecule #17: Small nuclear ribonucleoprotein E
+Macromolecule #18: Small nuclear ribonucleoprotein G
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #20: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #21: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #22: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~...
+Macromolecule #23: ZINC ION
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.5 mg/mL |
---|---|
Buffer | pH: 7.9 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER / Details: Initial model from CryoSparc |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 485418 |