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- EMDB-30643: Cryo-EM structure of the pre-mRNA-loaded DEAH-box ATPase/helicase... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30643 | |||||||||
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Title | Cryo-EM structure of the pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 in complex with Spp2 | |||||||||
![]() | EM map of Prp2 region in the Bact complex | |||||||||
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![]() | RNA splicing / spliceosome / Bact complex / Prp2 / Spp2 / DEAH-box ATPase/helicase / SPLICING | |||||||||
Function / homology | ![]() snoRNA splicing / generation of catalytic spliceosome for first transesterification step / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / ATPase activator activity / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity ...snoRNA splicing / generation of catalytic spliceosome for first transesterification step / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / ATPase activator activity / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.2 Å | |||||||||
![]() | Bai R / Wan R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Qi Jia / Jianlin Lei / Yigong Shi / ![]() Abstract: Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the ...Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu from the N half and Arg from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12 KB 12 KB | Display Display | ![]() |
Images | ![]() | 67.2 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dd3MC ![]() 7dcoC ![]() 7dcpC ![]() 7dcqC ![]() 7dcrC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | EM map of Prp2 region in the Bact complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : the complex of pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 and ...
Entire | Name: the complex of pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 and its coactivator Spp2 |
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Components |
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-Supramolecule #1: the complex of pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 and ...
Supramolecule | Name: the complex of pre-mRNA-loaded DEAH-box ATPase/helicase Prp2 and its coactivator Spp2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: PRP2 isoform 1
Macromolecule | Name: PRP2 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 99.947492 KDa |
Sequence | String: MSSITSETGK RRVKRTYEVT RQNDNAVRIE PSSLGEEEDK EAKDKNSALQ LKRSRYDPNK VFSNTNQGPE KNNLKGEQLG SQKKSSKYD EKITSNNELT TKKGLLGDSE NETKYASSNS KFNVEVTHKI KNAKEIDKIN RQRMWEEQQL RNAMAGQSDH P DDITLEGS ...String: MSSITSETGK RRVKRTYEVT RQNDNAVRIE PSSLGEEEDK EAKDKNSALQ LKRSRYDPNK VFSNTNQGPE KNNLKGEQLG SQKKSSKYD EKITSNNELT TKKGLLGDSE NETKYASSNS KFNVEVTHKI KNAKEIDKIN RQRMWEEQQL RNAMAGQSDH P DDITLEGS DKYDYVFDTD AMIDYTNEED DLLPEEKLQY EARLAQALET EEKRILTIQE ARKLLPVHQY KDELLQEIKK NQ VLIIMGE TGSGKTTQLP QYLVEDGFTD QGKLQIAITQ PRRVAATSVA ARVADEMNVV LGKEVGYQIR FEDKTTPNKT VLK YMTDGM LLREFLTDSK LSKYSCIMID EAHERTLATD ILIGLLKDIL PQRPTLKLLI SSATMNAKKF SEFFDNCPIF NVPG RRYPV DIHYTLQPEA NYIHAAITTI FQIHTTQSLP GDILVFLTGQ EEIERTKTKL EEIMSKLGSR TKQMIITPIY ANLPQ EQQL KIFQPTPENC RKVVLATNIA ETSLTIDGIR YVIDPGFVKE NSYVPSTGMT QLLTVPCSRA SVDQRAGRAG RVGPGK CFR IFTKWSYLHE LELMPKPEIT RTNLSNTVLL LLSLGVTDLI KFPLMDKPSI PTLRKSLENL YILGALNSKG TITRLGK MM CEFPCEPEFA KVLYTAATHE QCQGVLEECL TIVSMLHETP SLFIGQKRDA AASVLSEVES DHILYLEIFN QWRNSKFS R SWCQDHKIQF KTMLRVRNIR NQLFRCSEKV GLVEKNDQAR MKIGNIAGYI NARITRCFIS GFPMNIVQLG PTGYQTMGR SSGGLNVSVH PTSILFVNHK EKAQRPSKYV LYQQLMLTSK EFIRDCLVIP KEEWLIDMVP QIFKDLIDDK TNRGRR UniProtKB: PRP2 isoform 1 |
-Macromolecule #2: Pre-mRNA-splicing factor SPP2
Macromolecule | Name: Pre-mRNA-splicing factor SPP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.685377 KDa |
Sequence | String: MSKFSLKLGS KTLKKNISKK TKKKNSLQKA NLFDWDDAET ASLSHKPQSK IKIQSIDKFD LDEESSSKKK LVIKLSENAD TKKNDAPLV EYVTEKEYNE VPVEEFGDAL LRGMGWESDS EQDSKGDKTQ SRNKDVSNVS QIHPDGLGIG AKLNKAINVE E ASFMPVVK IDKITGTKVD DDKKNKS UniProtKB: Pre-mRNA-splicing factor SPP2 |
-Macromolecule #3: pre-mRNA
Macromolecule | Name: pre-mRNA / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.710535 KDa |
Sequence | String: UUUUUUUUU |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Staining | Type: NEGATIVE / Material: Uranyl Acetate |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 556393 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |