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- PDB-7abh: Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) -

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Entry
Database: PDB / ID: 7abh
TitleHuman pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)
Components
  • (Splicing factor 3A subunit ...) x 2
  • (Splicing factor 3B subunit ...) x 6
  • Cell division cycle 5-like protein
  • DNA/RNA-binding protein KIN17
  • MINX M3 pre-mRNA
  • PHD finger-like domain-containing protein 5A
  • RNA-binding motif protein, X-linked 2
  • Serine/arginine repetitive matrix protein 1
  • Smad nuclear-interacting protein 1
  • U2 snRNA
KeywordsSPLICING / Complex / spliceosome / catalytic activation
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / miRNA processing / splicing factor binding / U12-type spliceosomal complex / mRNA 3'-end processing / RNA splicing, via transesterification reactions / blastocyst formation / regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome ...U11/U12 snRNP / B-WICH complex / miRNA processing / splicing factor binding / U12-type spliceosomal complex / mRNA 3'-end processing / RNA splicing, via transesterification reactions / blastocyst formation / regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / SAGA complex / RHOBTB1 GTPase cycle / RNA Polymerase II Transcription Termination / U2 snRNP / WD40-repeat domain binding / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / transcription regulator inhibitor activity / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / regulation of RNA splicing / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / Prp19 complex / U2 snRNA binding / regulation of DNA repair / RHOBTB2 GTPase cycle / Protein methylation / negative regulation of canonical NF-kappaB signal transduction / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA damage checkpoint signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / stem cell differentiation / spliceosomal complex / negative regulation of protein catabolic process / mRNA splicing, via spliceosome / B-WICH complex positively regulates rRNA expression / positive regulation of neuron projection development / nuclear matrix / mRNA processing / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA recombination / DNA replication / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / chromatin remodeling / intracellular membrane-bounded organelle / DNA repair / mRNA binding / DNA damage response / regulation of transcription by RNA polymerase II / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / KIN17 WH-like domain / KN17 SH3-like domain / Domain of Kin17 curved DNA-binding protein / : / Ist3-like, RNA recognition motif ...DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / KIN17 WH-like domain / KN17 SH3-like domain / Domain of Kin17 curved DNA-binding protein / : / Ist3-like, RNA recognition motif / : / SF3B6, RNA recognition motif / : / PWI domain superfamily / PWI domain / PWI domain profile. / SF3B4, RNA recognition motif 2 / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Cactus-binding C-terminus of cactin protein / : / Replication stress response SDE2 C-terminal / PWI domain / PWI, domain in splicing factors / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / SF3B4, RNA recognition motif 1 / : / Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1 / : / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / Zinc-finger of C2H2 type / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / : / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / Myb-like DNA-binding domain / : / PPP2R1A-like HEAT repeat / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Myb-type HTH DNA-binding domain profile. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / RSE1/DDB1/CPSF1 first beta-propeller / Myb domain / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / SMAD/FHA domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Homeobox-like domain superfamily / Armadillo-like helical / Armadillo-type fold / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / DNA/RNA-binding protein KIN17 / Splicing factor 3B subunit 1 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 ...: / RNA / RNA (> 10) / RNA (> 100) / DNA/RNA-binding protein KIN17 / Splicing factor 3B subunit 1 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / Splicing factor 3A subunit 2 / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Smad nuclear-interacting protein 1 / Cell division cycle 5-like protein / Splicing factor 3B subunit 5 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsTownsend, C. / Kastner, B. / Leelaram, M.N. / Bertram, K. / Stark, H. / Luehrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)860 Germany
CitationJournal: Science / Year: 2020
Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
Authors: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway ...Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.
History
DepositionSep 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
L: Cell division cycle 5-like protein
y: PHD finger-like domain-containing protein 5A
Z: MINX M3 pre-mRNA
F: Splicing factor 3A subunit 2
4: Splicing factor 3A subunit 3
u: Splicing factor 3B subunit 1
T: Splicing factor 3B subunit 2
E: Splicing factor 3B subunit 3
w: Splicing factor 3B subunit 4
x: Splicing factor 3B subunit 5
z: Splicing factor 3B subunit 6
0: Smad nuclear-interacting protein 1
1: RNA-binding motif protein, X-linked 2
Y: Serine/arginine repetitive matrix protein 1
2: U2 snRNA
7: DNA/RNA-binding protein KIN17


Theoretical massNumber of molelcules
Total (without water)1,029,67116
Polymers1,029,67116
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules Ly01Y7

#1: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q99459
#2: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q7RTV0
#12: Protein Smad nuclear-interacting protein 1 / FHA domain-containing protein SNIP1


Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q8TAD8
#13: Protein RNA-binding motif protein, X-linked 2


Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q9Y388
#14: Protein Serine/arginine repetitive matrix protein 1 / SR-related nuclear matrix protein of 160 kDa / SRm160 / Ser/Arg-related nuclear matrix protein


Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q8IYB3
#16: Protein DNA/RNA-binding protein KIN17 / Binding to curved DNA / KIN / antigenic determinant of recA protein homolog


Mass: 45453.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: O60870

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RNA chain , 2 types, 2 molecules Z2

#3: RNA chain MINX M3 pre-mRNA


Mass: 73712.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: RNA chain U2 snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: GenBank: 36516

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Splicing factor 3A subunit ... , 2 types, 2 molecules F4

#4: Protein Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q15428
#5: Protein Splicing factor 3A subunit 3 / SF3a60 / Spliceosome-associated protein 61 / SAP 61


Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q12874

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Splicing factor 3B subunit ... , 6 types, 6 molecules uTEwxz

#6: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: O75533
#7: Protein Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145 / Spliceosome-associated protein 145 / SAP 145


Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q13435
#8: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q15393
#9: Protein Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49


Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q15427
#10: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q9BWJ5
#11: Protein Splicing factor 3B subunit 6 / Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / ...Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / 14-kDa / Splicing factor 3b / subunit 6 / 14kDa


Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q9Y3B4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)COMPLEXall0MULTIPLE SOURCES
2Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion)COMPLEX#1-#2, #4-#161NATURAL
3MINX M3 pre-mRNACOMPLEX#31RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
33synthetic construct (others)32630
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 1 sec. / Electron dose: 2.25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39336 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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