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- EMDB-11694: Human pre-Bact-1 spliceosome core structure -

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Basic information

Entry
Database: EMDB / ID: EMD-11694
TitleHuman pre-Bact-1 spliceosome core structure
Map dataSharpened/masked map for pre-Bact-1 core structure.
Sample
  • Complex: pre-Bact-1 spliceosomal complex
    • Complex: pre-Bact-1 spliceosomal complex
      • Protein or peptide: x 12 types
      • RNA: x 2 types
    • Complex: MINX M3 RNA
      • RNA: x 1 types
  • Ligand: x 3 types
KeywordsComplex / spliceosome / catalytic activation / splicing
Function / homology
Function and homology information


microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / host-mediated activation of viral transcription / U2-type precatalytic spliceosome ...microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / positive regulation of vitamin D receptor signaling pathway / mRNA cis splicing, via spliceosome / nuclear vitamin D receptor binding / RNA polymerase binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Notch binding / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / positive regulation of neurogenesis / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / NOTCH3 Intracellular Domain Regulates Transcription / ubiquitin-like protein conjugating enzyme binding / WW domain binding / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / Notch-HLH transcription pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein localization to nucleus / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / Cajal body / U1 snRNA binding / retinoic acid receptor signaling pathway / U4/U6 x U5 tri-snRNP complex / cellular response to retinoic acid / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor binding / transcription coregulator activity / spliceosomal complex / positive regulation of transcription elongation by RNA polymerase II / response to cocaine / Downregulation of SMAD2/3:SMAD4 transcriptional activity / protein modification process / mRNA splicing, via spliceosome / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / protein tag activity / nuclear matrix / fibrillar center / mRNA processing / rRNA processing / transcription corepressor activity / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / single-stranded DNA binding / microtubule cytoskeleton / cellular response to lipopolysaccharide / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / nuclear body / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / GTPase activity / centrosome / regulation of transcription by RNA polymerase II / GTP binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
WW domain binding protein 11 / WW domain binding protein 11 / Ubiquitin-like modifier Hub1/Ubl5 / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 ...WW domain binding protein 11 / WW domain binding protein 11 / Ubiquitin-like modifier Hub1/Ubl5 / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / Transcription elongation regulator 1-like / PRP38 family / TCERG1 WW domain / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / G10 protein signature 2. / BUD31/G10-related, conserved site / G10 protein signature 1. / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / G10 protein / Pre-mRNA-splicing factor BUD31 / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Elongation Factor G, domain II / Elongation Factor G, domain III / WW domain / WW/rsp5/WWP domain signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Zinc finger C2H2 superfamily / Ubiquitin family / Small GTP-binding protein domain / Ubiquitin-like domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribonuclease H-like superfamily / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription elongation regulator 1 / Pleiotropic regulator 1 / Protein BUD31 homolog / Microfibrillar-associated protein 1 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor 38A / Zinc finger matrin-type protein 2 / Ubiquitin-like protein 5 ...Transcription elongation regulator 1 / Pleiotropic regulator 1 / Protein BUD31 homolog / Microfibrillar-associated protein 1 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor 38A / Zinc finger matrin-type protein 2 / Ubiquitin-like protein 5 / Spliceosome-associated protein CWC15 homolog / WW domain-binding protein 11
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsTownsend C / Kastner B
Funding support Germany, 1 items
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, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7abf
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11694.png

Downloads & links

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Map

FileDownload / File: emd_11694.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened/masked map for pre-Bact-1 core structure.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 384 pix.
= 445.44 Å		1.16 Å/pix.
x 384 pix.
= 445.44 Å		1.16 Å/pix.
x 384 pix.
= 445.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.06255429 - 0.13082597
Average (Standard dev.)0.00021495222 (±0.0029636216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 445.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z445.440445.440445.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0630.1310.000

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Supplemental data

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Sample components

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Entire : pre-Bact-1 spliceosomal complex

EntireName: pre-Bact-1 spliceosomal complex
Components
  • Complex: pre-Bact-1 spliceosomal complex
    • Complex: pre-Bact-1 spliceosomal complex
      • Protein or peptide: Protein BUD31 homolog
      • Protein or peptide: Pre-mRNA-splicing factor 38A
      • Protein or peptide: Pre-mRNA-processing-splicing factor 8
      • Protein or peptide: 116 kDa U5 small nuclear ribonucleoprotein component
      • Protein or peptide: Zinc finger matrin-type protein 2
      • Protein or peptide: Ubiquitin-like protein 5
      • Protein or peptide: Spliceosome-associated protein CWC15 homolog
      • RNA: U5 small nuclear RNA
      • RNA: U6 small nuclear RNA
      • Protein or peptide: WW domain-binding protein 11
      • Protein or peptide: SNW domain-containing protein 1
      • Protein or peptide: Pleiotropic regulator 1
      • Protein or peptide: Microfibrillar-associated protein 1
      • Protein or peptide: Transcription elongation regulator 1
    • Complex: MINX M3 RNA
      • RNA: MINX M3 RNA
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: pre-Bact-1 spliceosomal complex

SupramoleculeName: pre-Bact-1 spliceosomal complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15

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Supramolecule #2: pre-Bact-1 spliceosomal complex

SupramoleculeName: pre-Bact-1 spliceosomal complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12, #14-#15
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: MINX M3 RNA

SupramoleculeName: MINX M3 RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Protein BUD31 homolog

MacromoleculeName: Protein BUD31 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.03285 KDa
SequenceString:
MPKVKRSRKA PPDGWELIEP TLDELDQKMR EAETEPHEGK RKVESLWPIF RIHHQKTRYI FDLFYKRKAI SRELYEYCIK EGYADKNLI AKWKKQGYEN LCCLRCIQTR DTNFGTNCIC RVPKSKLEVG RIIECTHCGC RGCSG

UniProtKB: Protein BUD31 homolog

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Macromolecule #2: Pre-mRNA-splicing factor 38A

MacromoleculeName: Pre-mRNA-splicing factor 38A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.563863 KDa
SequenceString: MANRTVKDAH SIHGTNPQYL VEKIIRTRIY ESKYWKEECF GLTAELVVDK AMELRFVGGV YGGNIKPTPF LCLTLKMLQI QPEKDIIVE FIKNEDFKYV RMLGALYMRL TGTAIDCYKY LEPLYNDYRK IKSQNRNGEF ELMHVDEFID ELLHSERVCD I ILPRLQKR ...String:
MANRTVKDAH SIHGTNPQYL VEKIIRTRIY ESKYWKEECF GLTAELVVDK AMELRFVGGV YGGNIKPTPF LCLTLKMLQI QPEKDIIVE FIKNEDFKYV RMLGALYMRL TGTAIDCYKY LEPLYNDYRK IKSQNRNGEF ELMHVDEFID ELLHSERVCD I ILPRLQKR YVLEEAEQLE PRVSALEEDM DDVESSEEEE EEDEKLERVP SPDHRRRSYR DLDKPRRSPT LRYRRSRSRS PR RRSRSPK RRSPSPRRER HRSKSPRRHR SRSRDRRHRS RSKSPGHHRS HRHRSHSKSP ERSKKSHKKS RRGNE

UniProtKB: Pre-mRNA-splicing factor 38A

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Macromolecule #3: Pre-mRNA-processing-splicing factor 8

MacromoleculeName: Pre-mRNA-processing-splicing factor 8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 273.97425 KDa
SequenceString: MAGVFPYRGP GNPVPGPLAP LPDYMSEEKL QEKARKWQQL QAKRYAEKRK FGFVDAQKED MPPEHVRKII RDHGDMTNRK FRHDKRVYL GALKYMPHAV LKLLENMPMP WEQIRDVPVL YHITGAISFV NEIPWVIEPV YISQWGSMWI MMRREKRDRR H FKRMRFPP ...String:
MAGVFPYRGP GNPVPGPLAP LPDYMSEEKL QEKARKWQQL QAKRYAEKRK FGFVDAQKED MPPEHVRKII RDHGDMTNRK FRHDKRVYL GALKYMPHAV LKLLENMPMP WEQIRDVPVL YHITGAISFV NEIPWVIEPV YISQWGSMWI MMRREKRDRR H FKRMRFPP FDDEEPPLDY ADNILDVEPL EAIQLELDPE EDAPVLDWFY DHQPLRDSRK YVNGSTYQRW QFTLPMMSTL YR LANQLLT DLVDDNYFYL FDLKAFFTSK ALNMAIPGGP KFEPLVRDIN LQDEDWNEFN DINKIIIRQP IRTEYKIAFP YLY NNLPHH VHLTWYHTPN VVFIKTEDPD LPAFYFDPLI NPISHRHSVK SQEPLPDDDE EFELPEFVEP FLKDTPLYTD NTAN GIALL WAPRPFNLRS GRTRRALDIP LVKNWYREHC PAGQPVKVRV SYQKLLKYYV LNALKHRPPK AQKKRYLFRS FKATK FFQS TKLDWVEVGL QVCRQGYNML NLLIHRKNLN YLHLDYNFNL KPVKTLTTKE RKKSRFGNAF HLCREVLRLT KLVVDS HVQ YRLGNVDAFQ LADGLQYIFA HVGQLTGMYR YKYKLMRQIR MCKDLKHLIY YRFNTGPVGK GPGCGFWAAG WRVWLFF MR GITPLLERWL GNLLARQFEG RHSKGVAKTV TKQRVESHFD LELRAAVMHD ILDMMPEGIK QNKARTILQH LSEAWRCW K ANIPWKVPGL PTPIENMILR YVKAKADWWT NTAHYNRERI RRGATVDKTV CKKNLGRLTR LYLKAEQERQ HNYLKDGPY ITAEEAVAVY TTTVHWLESR RFSPIPFPPL SYKHDTKLLI LALERLKEAY SVKSRLNQSQ REELGLIEQA YDNPHEALSR IKRHLLTQR AFKEVGIEFM DLYSHLVPVY DVEPLEKITD AYLDQYLWYE ADKRRLFPPW IKPADTEPPP LLVYKWCQGI N NLQDVWET SEGECNVMLE SRFEKMYEKI DLTLLNRLLR LIVDHNIADY MTAKNNVVIN YKDMNHTNSY GIIRGLQFAS FI VQYYGLV MDLLVLGLHR ASEMAGPPQM PNDFLSFQDI ATEAAHPIRL FCRYIDRIHI FFRFTADEAR DLIQRYLTEH PDP NNENIV GYNNKKCWPR DARMRLMKHD VNLGRAVFWD IKNRLPRSVT TVQWENSFVS VYSKDNPNLL FNMCGFECRI LPKC RTSYE EFTHKDGVWN LQNEVTKERT AQCFLRVDDE SMQRFHNRVR QILMASGSTT FTKIVNKWNT ALIGLMTYFR EAVVN TQEL LDLLVKCENK IQTRIKIGLN SKMPSRFPPV VFYTPKELGG LGMLSMGHVL IPQSDLRWSK QTDVGITHFR SGMSHE EDQ LIPNLYRYIQ PWESEFIDSQ RVWAEYALKR QEAIAQNRRL TLEDLEDSWD RGIPRINTLF QKDRHTLAYD KGWRVRT DF KQYQVLKQNP FWWTHQRHDG KLWNLNNYRT DMIQALGGVE GILEHTLFKG TYFPTWEGLF WEKASGFEES MKWKKLTN A QRSGLNQIPN RRFTLWWSPT INRANVYVGF QVQLDLTGIF MHGKIPTLKI SLIQIFRAHL WQKIHESIVM DLCQVFDQE LDALEIETVQ KETIHPRKSY KMNSSCADIL LFASYKWNVS RPSLLADSKD VMDSTTTQKY WIDIQLRWGD YDSHDIERYA RAKFLDYTT DNMSIYPSPT GVLIAIDLAY NLHSAYGNWF PGSKPLIQQA MAKIMKANPA LYVLRERIRK GLQLYSSEPT E PYLSSQNY GELFSNQIIW FVDDTNVYRV TIHKTFEGNL TTKPINGAIF IFNPRTGQLF LKIIHTSVWA GQKRLGQLAK WK TAEEVAA LIRSLPVEEQ PKQIIVTRKG MLDPLEVHLL DFPNIVIKGS ELQLPFQACL KVEKFGDLIL KATEPQMVLF NLY DDWLKT ISSYTAFSRL ILILRALHVN NDRAKVILKP DKTTITEPHH IWPTLTDEEW IKVEVQLKDL ILADYGKKNN VNVA SLTQS EIRDIILGME ISAPSQQRQQ IAEIEKQTKE QSQLTATQTR TVNKHGDEII TSTTSNYETQ TFSSKTEWRV RAISA ANLH LRTNHIYVSS DDIKETGYTY ILPKNVLKKF ICISDLRAQI AGYLYGVSPP DNPQVKEIRC IVMVPQWGTH QTVHLP GQL PQHEYLKEME PLGWIHTQPN ESPQLSPQDV TTHAKIMADN PSWDGEKTII ITCSFTPGSC TLTAYKLTPS GYEWGRQ NT DKGNNPKGYL PSHYERVQML LSDRFLGFFM VPAQSSWNYN FMGVRHDPNM KYELQLANPK EFYHEVHRPS HFLNFALL Q EGEVYSADRE DLYA

UniProtKB: Pre-mRNA-processing-splicing factor 8

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Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component

MacromoleculeName: 116 kDa U5 small nuclear ribonucleoprotein component / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.560625 KDa
SequenceString: MDTDLYDEFG NYIGPELDSD EDDDELGRET KDLDEMDDDD DDDDVGDHDD DHPGMEVVLH EDKKYYPTAE EVYGPEVETI VQEEDTQPL TEPIIKPVKT KKFTLMEQTL PVTVYEMDFL ADLMDNSELI RNVTLCGHLH HGKTCFVDCL IEQTHPEIRK R YDQDLCYT ...String:
MDTDLYDEFG NYIGPELDSD EDDDELGRET KDLDEMDDDD DDDDVGDHDD DHPGMEVVLH EDKKYYPTAE EVYGPEVETI VQEEDTQPL TEPIIKPVKT KKFTLMEQTL PVTVYEMDFL ADLMDNSELI RNVTLCGHLH HGKTCFVDCL IEQTHPEIRK R YDQDLCYT DILFTEQERG VGIKSTPVTV VLPDTKGKSY LFNIMDTPGH VNFSDEVTAG LRISDGVVLF IDAAEGVMLN TE RLIKHAV QERLAVTVCI NKIDRLILEL KLPPTDAYYK LRHIVDEVNG LISMYSTDEN LILSPLLGNV CFSSSQYSIC FTL GSFAKI YADTFGDINY QEFAKRLWGD IYFNPKTRKF TKKAPTSSSQ RSFVEFILEP LYKILAQVVG DVDTSLPRTL DELG IHLTK EELKLNIRPL LRLVCKKFFG EFTGFVDMCV QHIPSPKVGA KPKIEHTYTG GVDSDLGEAM SDCDPDGPLM CHTTK MYST DDGVQFHAFG RVLSGTIHAG QPVKVLGENY TLEDEEDSQI CTVGRLWISV ARYHIEVNRV PAGNWVLIEG VDQPIV KTA TITEPRGNEE AQIFRPLKFN TTSVIKIAVE PVNPSELPKM LDGLRKVNKS YPSLTTKVEE SGEHVILGTG ELYLDCV MH DLRKMYSEID IKVADPVVTF CETVVETSSL KCFAETPNKK NKITMIAEPL EKGLAEDIEN EVVQITWNRK KLGEFFQT K YDWDLLAARS IWAFGPDATG PNILVDDTLP SEVDKALLGS VKDSIVQGFQ WGTREGPLCD ELIRNVKFKI LDAVVAQEP LHRGGGQIIP TARRVVYSAF LMATPRLMEP YYFVEVQAPA DCVSAVYTVL ARRRGHVTQD APIPGSPLYT IKAFIPAIDS FGFETDLRT HTQGQAFSLS VFHHWQIVPG DPLDKSIVIR PLEPQPAPHL AREFMIKTRR RKGLSEDVSI SKFFDDPMLL E LAKQDVVL NYPM

UniProtKB: 116 kDa U5 small nuclear ribonucleoprotein component

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Macromolecule #5: Zinc finger matrin-type protein 2

MacromoleculeName: Zinc finger matrin-type protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.664047 KDa
SequenceString: MASGSGTKNL DFRRKWDKDE YEKLAEKRLT EEREKKDGKP VQPVKRELLR HRDYKVDLES KLGKTIVITK TTPQSEMGGY YCNVCDCVV KDSINFLDHI NGKKHQRNLG MSMRVERSTL DQVKKRFEVN KKKMEEKQKD YDFEERMKEL REEEEKAKAY K KEKQKEKK ...String:
MASGSGTKNL DFRRKWDKDE YEKLAEKRLT EEREKKDGKP VQPVKRELLR HRDYKVDLES KLGKTIVITK TTPQSEMGGY YCNVCDCVV KDSINFLDHI NGKKHQRNLG MSMRVERSTL DQVKKRFEVN KKKMEEKQKD YDFEERMKEL REEEEKAKAY K KEKQKEKK RRAEEDLTFE EDDEMAAVMG FSGFGSTKKS Y

UniProtKB: Zinc finger matrin-type protein 2

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Macromolecule #6: Ubiquitin-like protein 5

MacromoleculeName: Ubiquitin-like protein 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.560945 KDa
SequenceString:
MIEVVCNDRL GKKVRVKCNT DDTIGDLKKL IAAQTGTRWN KIVLKKWYTI FKDHVSLGDY EIHDGMNLEL YYQ

UniProtKB: Ubiquitin-like protein 5

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Macromolecule #7: Spliceosome-associated protein CWC15 homolog

MacromoleculeName: Spliceosome-associated protein CWC15 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.674447 KDa
SequenceString: MTTAARPTFE PARGGRGKGE GDLSQLSKQY SSRDLPSHTK IKYRQTTQDA PEEVRNRDFR RELEERERAA AREKNRDRPT REHTTSSSV SKKPRLDQIP AANLDADDPL TDEEDEDFEE ESDDDDTAAL LAELEKIKKE RAEEQARKEQ EQKAEEERIR M ENILSGNP ...String:
MTTAARPTFE PARGGRGKGE GDLSQLSKQY SSRDLPSHTK IKYRQTTQDA PEEVRNRDFR RELEERERAA AREKNRDRPT REHTTSSSV SKKPRLDQIP AANLDADDPL TDEEDEDFEE ESDDDDTAAL LAELEKIKKE RAEEQARKEQ EQKAEEERIR M ENILSGNP LLNLTGPSQP QANFKVKRRW DDDVVFKNCA KGVDDQKKDK RFVNDTLRSE FHKKFMEKYI K

UniProtKB: Spliceosome-associated protein CWC15 homolog

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Macromolecule #10: WW domain-binding protein 11

MacromoleculeName: WW domain-binding protein 11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.098641 KDa
SequenceString: MGRRSTSSTK SGKFMNPTDQ ARKEARKREL KKNKKQRMMV RAAVLKMKDP KQIIRDMEKL DEMEFNPVQQ PQLNEKVLKD KRKKLRETF ERILRLYEKE NPDIYKELRK LEVEYEQKRA QLSQYFDAVK NAQHVEVESI PLPDMPHAPS NILIQDIPLP G AQPPSILK ...String:
MGRRSTSSTK SGKFMNPTDQ ARKEARKREL KKNKKQRMMV RAAVLKMKDP KQIIRDMEKL DEMEFNPVQQ PQLNEKVLKD KRKKLRETF ERILRLYEKE NPDIYKELRK LEVEYEQKRA QLSQYFDAVK NAQHVEVESI PLPDMPHAPS NILIQDIPLP G AQPPSILK KTSAYGPPTR AVSILPLLGH GVPRLPPGRK PPGPPPGPPP PQVVQMYGRK VGFALDLPPR RRDEDMLYSP EL AQRGHDD DVSSTSEDDG YPEDMDQDKH DDSTDDSDTD KSDGESDGDE FVHRDNGERD NNEEKKSGLS VRFADMPGKS RKK KKNMKE LTPLQAMMLR MAGQEIPEEG REVEEFSEDD DEDDSDDSEA EKQSQKQHKE ESHSDGTSTA SSQQQAPPQS VPPS QIQAP PMPGPPPLGP PPAPPLRPPG PPTGLPPGPP PGAPPFLRPP GMPGLRGPLP RLLPPGPPPG RPPGPPPGPP PGLPP GPPP RGPPPRLPPP APPGIPPPRP GMMRPPLVPP LGPAPPGLFP PAPLPNPGVL SAPPNLIQRP KADDTSAATI EKKATA TIS AKPQITNPKA EITRFVPTAL RVRRENKGAT AAPQRKSEDD SAVPLAKAAP KSGPSVPVSV QTKDDVYEAF MKEMEGL L

UniProtKB: WW domain-binding protein 11

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Macromolecule #11: SNW domain-containing protein 1

MacromoleculeName: SNW domain-containing protein 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.610703 KDa
SequenceString: MALTSFLPAP TQLSQDQLEA EEKARSQRSR QTSLVSSRRE PPPYGYRKGW IPRLLEDFGD GGAFPEIHVA QYPLDMGRKK KMSNALAIQ VDSEGKIKYD AIARQGQSKD KVIYSKYTDL VPKEVMNADD PDLQRPDEEA IKEITEKTRV ALEKSVSQKV A AAMPVRAA ...String:
MALTSFLPAP TQLSQDQLEA EEKARSQRSR QTSLVSSRRE PPPYGYRKGW IPRLLEDFGD GGAFPEIHVA QYPLDMGRKK KMSNALAIQ VDSEGKIKYD AIARQGQSKD KVIYSKYTDL VPKEVMNADD PDLQRPDEEA IKEITEKTRV ALEKSVSQKV A AAMPVRAA DKLAPAQYIR YTPSQQGVAF NSGAKQRVIR MVEMQKDPME PPRFKINKKI PRGPPSPPAP VMHSPSRKMT VK EQQEWKI PPCISNWKNA KGYTIPLDKR LAADGRGLQT VHINENFAKL AEALYIADRK AREAVEMRAQ VERKMAQKEK EKH EEKLRE MAQKARERRA GIKTHVEKED GEARERDEIR HDRRKERQHD RNLSRAAPDK RSKLQRNENR DISEVIALGV PNPR TSNEV QYDQRLFNQS KGMDSGFAGG EDEIYNVYDQ AWRGGKDMAQ SIYRPSKNLD KDMYGDDLEA RIKTNRFVPD KEFSG SDRR QRGREGPVQF EEDPFGLDKF LEEAKQHGGS KRPSDSSRPK EHEHEGKKRR KE

UniProtKB: SNW domain-containing protein 1

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Macromolecule #12: Pleiotropic regulator 1

MacromoleculeName: Pleiotropic regulator 1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.280758 KDa
SequenceString: MVEEVQKHSV HTLVFRSLKR THDMFVADNG KPVPLDEESH KRKMAIKLRN EYGPVLHMPT SKENLKEKGP QNATDSYVHK QYPANQGQE VEYFVAGTHP YPPGPGVALT ADTKIQRMPS ESAAQSLAVA LPLQTKADAN RTAPSGSEYR HPGASDRPQP T AMNSIVME ...String:
MVEEVQKHSV HTLVFRSLKR THDMFVADNG KPVPLDEESH KRKMAIKLRN EYGPVLHMPT SKENLKEKGP QNATDSYVHK QYPANQGQE VEYFVAGTHP YPPGPGVALT ADTKIQRMPS ESAAQSLAVA LPLQTKADAN RTAPSGSEYR HPGASDRPQP T AMNSIVME TGNTKNSALM AKKAPTMPKP QWHPPWKLYR VISGHLGWVR CIAVEPGNQW FVTGSADRTI KIWDLASGKL KL SLTGHIS TVRGVIVSTR SPYLFSCGED KQVKCWDLEY NKVIRHYHGH LSAVYGLDLH PTIDVLVTCS RDSTARIWDV RTK ASVHTL SGHTNAVATV RCQAAEPQII TGSHDTTIRL WDLVAGKTRV TLTNHKKSVR AVVLHPRHYT FASGSPDNIK QWKF PDGSF IQNLSGHNAI INTLTVNSDG VLVSGADNGT MHLWDWRTGY NFQRVHAAVQ PGSLDSESGI FACAFDQSES RLLTA EADK TIKVYREDDT ATEETHPVSW KPEIIKRKRF

UniProtKB: Pleiotropic regulator 1

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Macromolecule #14: Microfibrillar-associated protein 1

MacromoleculeName: Microfibrillar-associated protein 1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.050527 KDa
SequenceString: MSVPSALMKQ PPIQSTAGAV PVRNEKGEIS MEKVKVKRYV SGKRPDYAPM ESSDEEDEEF QFIKKAKEQE AEPEEQEEDS SSDPRLRRL QNRISEDVEE RLARHRKIVE PEVVGESDSE VEGDAWRMER EDSSEEEEEE IDDEEIERRR GMMRQRAQER K NEEMEVME ...String:
MSVPSALMKQ PPIQSTAGAV PVRNEKGEIS MEKVKVKRYV SGKRPDYAPM ESSDEEDEEF QFIKKAKEQE AEPEEQEEDS SSDPRLRRL QNRISEDVEE RLARHRKIVE PEVVGESDSE VEGDAWRMER EDSSEEEEEE IDDEEIERRR GMMRQRAQER K NEEMEVME VEDEGRSGEE SESESEYEEY TDSEDEMEPR LKPVFIRKKD RVTVQEREAE ALKQKELEQE AKRMAEERRK YT LKIVEEE TKKELEENKR SLAALDALNT DDENDEEEYE AWKVRELKRI KRDREDREAL EKEKAEIERM RNLTEEERRA ELR ANGKVI TNKAVKGKYK FLQKYYHRGA FFMDEDEEVY KRDFSAPTLE DHFNKTILPK VMQVKNFGRS GRTKYTHLVD QDTT SFDSA WGQESAQNTK FFKQKAAGVR DVFERPSAKK RKTT

UniProtKB: Microfibrillar-associated protein 1

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Macromolecule #15: Transcription elongation regulator 1

MacromoleculeName: Transcription elongation regulator 1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 121.87032 KDa
SequenceString: MAERGGDGGE SERFNPGELR MAQQQALRFR GPAPPPNAVM RGPPPLMRPP PPFGMMRGPP PPPRPPFGRP PFDPNMPPMP PPGGIPPPM GPPHLQRPPF MPPPMSSMPP PPGMMFPPGM PPVTAPGTPA LPPTEEIWVE NKTPDGKVYY YNARTRESAW T KPDGVKVI ...String:
MAERGGDGGE SERFNPGELR MAQQQALRFR GPAPPPNAVM RGPPPLMRPP PPFGMMRGPP PPPRPPFGRP PFDPNMPPMP PPGGIPPPM GPPHLQRPPF MPPPMSSMPP PPGMMFPPGM PPVTAPGTPA LPPTEEIWVE NKTPDGKVYY YNARTRESAW T KPDGVKVI QQSELTPMLA AQAQVQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQ AQVQAQV QAQVQAQAVG ASTPTTSSPA PAVSTSTSSS TPSSTTSTTT TATSVAQTVS TPTTQDQTPS SAVSVATPTV SVS TPAPTA TPVQTVPQPH PQTLPPAVPH SVPQPTTAIP AFPPVMVPPF RVPLPGMPIP LPGVLPGMAP PIVPMIHPQV AIAA SPATL AGATAVSEWT EYKTADGKTY YYNNRTLEST WEKPQELKEK EKLEEKIKEP IKEPSEEPLP METEEEDPKE EPIKE IKEE PKEEEMTEEE KAAQKAKPVA TAPIPGTPWC VVWTGDERVF FYNPTTRLSM WDRPDDLIGR ADVDKIIQEP PHKKGM EEL KKLRHPTPTM LSIQKWQFSM SAIKEEQELM EEINEDEPVK AKKRKRDDNK DIDSEKEAAM EAEIKAARER AIVPLEA RM KQFKDMLLER GVSAFSTWEK ELHKIVFDPR YLLLNPKERK QVFDQYVKTR AEEERREKKN KIMQAKEDFK KMMEEAKF N PRATFSEFAA KHAKDSRFKA IEKMKDREAL FNEFVAAARK KEKEDSKTRG EKIKSDFFEL LSNHHLDSQS RWSKVKDKV ESDPRYKAVD SSSMREDLFK QYIEKIAKNL DSEKEKELER QARIEASLRE REREVQKARS EQTKEIDRER EQHKREEAIQ NFKALLSDM VRSSDVSWSD TRRTLRKDHR WESGSLLERE EKEKLFNEHI EALTKKKREH FRQLLDETSA ITLTSTWKEV K KIIKEDPR CIKFSSSDRK KQREFEEYIR DKYITAKADF RTLLKETKFI TYRSKKLIQE SDQHLKDVEK ILQNDKRYLV LD CVPEERR KLIVAYVDDL DRRGPPPPPT ASEPTRRSTK

UniProtKB: Transcription elongation regulator 1

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Macromolecule #8: U5 small nuclear RNA

MacromoleculeName: U5 small nuclear RNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.908668 KDa
SequenceString:
AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAU UUUUUGAGCC UUGCCUUGGC AAGGCUA

GENBANK: GENBANK: X01691.1

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Macromolecule #9: U6 small nuclear RNA

MacromoleculeName: U6 small nuclear RNA / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.09827 KDa
SequenceString:
GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGU GAAGCGUUCC AUAUUUU

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Macromolecule #13: MINX M3 RNA

MacromoleculeName: MINX M3 RNA / type: rna / ID: 13 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 73.712359 KDa
SequenceString: GGGAGACGGA AUUCGAGCUC GCCCACUCUU GGAUCGGAAA CCCGUCGGCC UCCGAACGGU AAGAGCCUAG CAUGUAGAAC UGGUUACCU GCAGCCCAAG CUUGCUGCAC GUCUAGGGCG CAGUAGUCCA GGGUUUCCUU GAUGAUGUCA UACUUAUCCU G UCCCUUUU ...String:
GGGAGACGGA AUUCGAGCUC GCCCACUCUU GGAUCGGAAA CCCGUCGGCC UCCGAACGGU AAGAGCCUAG CAUGUAGAAC UGGUUACCU GCAGCCCAAG CUUGCUGCAC GUCUAGGGCG CAGUAGUCCA GGGUUUCCUU GAUGAUGUCA UACUUAUCCU G UCCCUUUU UUUUCCACAG CUCGCGGUUG AGGACAAACU CUUCGCGGUC UUUCCAGUGG GGAUCCAAUA UC

+
Macromolecule #16: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 16 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #17: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 2.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 84539
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7abf:
Human pre-Bact-1 spliceosome core structure

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