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- EMDB-0360: Saccharomyces cerevisiae spliceosomal E complex (UBC4) -

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Basic information

Entry
Database: EMDB / ID: EMD-0360
TitleSaccharomyces cerevisiae spliceosomal E complex (UBC4)
Map dataSpliceosomal E complex (UBC4)
Sample
  • Complex: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
    • Protein or peptide: x 19 types
    • RNA: x 2 types
  • Ligand: x 1 types
Keywordspre-mRNA splicing / spliceosome / E complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / nuclear cap binding complex / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex ...Processing of Intronless Pre-mRNAs / nuclear cap binding complex / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / snRNP binding / small nuclear ribonucleoprotein complex / mRNA 3'-end processing / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U1 snRNP / poly(U) RNA binding / response to osmotic stress / U2-type prespliceosome / Processing of Capped Intron-Containing Pre-mRNA / pre-mRNA 5'-splice site binding / Formation of the Early Elongation Complex / mRNA Capping / precatalytic spliceosome / RNA Polymerase II Pre-transcription Events / spliceosomal complex assembly / mRNA 5'-splice site recognition / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / nuclear-transcribed mRNA catabolic process / Prp19 complex / 7-methylguanosine mRNA capping / U5 snRNP / spliceosomal snRNP assembly / mRNA export from nucleus / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / mRNA binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / SNU71 RNA binding domain / SNU71 N-terminal / Pre-mRNA-processing factor Prp40 / U1 small nuclear ribonucleoprotein C / MIF4G-like, type 1 / MIF4G-like, type 2 ...Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / SNU71 RNA binding domain / SNU71 N-terminal / Pre-mRNA-processing factor Prp40 / U1 small nuclear ribonucleoprotein C / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / PRP39 C-terminal HAT repeat / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / : / U1-C, C2H2-type zinc finger / U1 zinc finger / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / PWI domain / PWI, domain in splicing factors / PRP39 N-terminal HAT repeat / : / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / Sm domain profile. / LSM domain superfamily / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Zinc finger C2H2 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing protein PRP40 / Nuclear cap-binding protein complex subunit 1 / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein F / Protein NAM8 ...U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing protein PRP40 / Nuclear cap-binding protein complex subunit 1 / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein F / Protein NAM8 / U1 small nuclear ribonucleoprotein 70 kDa homolog / Small nuclear ribonucleoprotein Sm D1 / U1 small nuclear ribonucleoprotein component PRP42 / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein Sm D2 / Protein LUC7 / Nuclear cap-binding protein subunit 2 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu S / Li X
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM126157 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM114178 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM071940 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI094386 United States
CitationJournal: Nature / Year: 2019
Title: A unified mechanism for intron and exon definition and back-splicing.
Authors: Xueni Li / Shiheng Liu / Lingdi Zhang / Aaron Issaian / Ryan C Hill / Sara Espinosa / Shasha Shi / Yanxiang Cui / Kalli Kappel / Rhiju Das / Kirk C Hansen / Z Hong Zhou / Rui Zhao /
Abstract: The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E ...The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes.
History
DepositionNov 27, 2018-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n7p
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0360.png

Downloads & links

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Map

FileDownload / File: emd_0360.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSpliceosomal E complex (UBC4)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 384 pix.
= 522.24 Å		1.36 Å/pix.
x 384 pix.
= 522.24 Å		1.36 Å/pix.
x 384 pix.
= 522.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.20593081 - 0.37101442
Average (Standard dev.)-0.00004524245 (±0.0076556755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 522.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z522.240522.240522.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2060.371-0.000

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Supplemental data

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Sample components

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Entire : Saccharomyces cerevisiae spliceosomal E complex (EBC4)

EntireName: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
Components
  • Complex: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
    • Protein or peptide: U1 small nuclear ribonucleoprotein 70 kDa homolog
    • Protein or peptide: U1 small nuclear ribonucleoprotein C
    • Protein or peptide: U1 small nuclear ribonucleoprotein A
    • Protein or peptide: U1 small nuclear ribonucleoprotein component PRP42
    • Protein or peptide: Pre-mRNA-processing factor 39
    • Protein or peptide: Protein NAM8
    • Protein or peptide: 56 kDa U1 small nuclear ribonucleoprotein component
    • Protein or peptide: U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71
    • Protein or peptide: Protein LUC7
    • Protein or peptide: Pre-mRNA-processing protein PRP40
    • Protein or peptide: Small nuclear ribonucleoprotein-associated protein B
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D2
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • RNA: U1 snRNA
    • RNA: UBC4 pre-mRNA
    • Protein or peptide: Nuclear cap-binding protein complex subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
  • Ligand: ZINC ION

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Supramolecule #1: Saccharomyces cerevisiae spliceosomal E complex (EBC4)

SupramoleculeName: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: U1 small nuclear ribonucleoprotein 70 kDa homolog

MacromoleculeName: U1 small nuclear ribonucleoprotein 70 kDa homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 34.506148 KDa
SequenceString: MNYNLSKYPD DVSRLFKPRP PLSYKRPTDY PYAKRQTNPN ITGVANLLST SLKHYMEEFP EGSPNNHLQR YEDIKLSKIK NAQLLDRRL QNWNPNVDPH IKDTDPYRTI FIGRLPYDLD EIELQKYFVK FGEIEKIRIV KDKITQKSKG YAFIVFKDPI S SKMAFKEI ...String:
MNYNLSKYPD DVSRLFKPRP PLSYKRPTDY PYAKRQTNPN ITGVANLLST SLKHYMEEFP EGSPNNHLQR YEDIKLSKIK NAQLLDRRL QNWNPNVDPH IKDTDPYRTI FIGRLPYDLD EIELQKYFVK FGEIEKIRIV KDKITQKSKG YAFIVFKDPI S SKMAFKEI GVHRGIQIKD RICIVDIERG RTVKYFKPRR LGGGLGGRGY SNRDSRLPGR FASASTSNPA ERNYAPRLPR RE TSSSAYS ADRYGSSTLD ARYRGNRPLL SAATPTAAVT SVYKSRNSRT RESQPAPKEA PDY

UniProtKB: U1 small nuclear ribonucleoprotein 70 kDa homolog

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Macromolecule #2: U1 small nuclear ribonucleoprotein C

MacromoleculeName: U1 small nuclear ribonucleoprotein C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.106016 KDa
SequenceString: MTRYYCEYCH SYLTHDTLSV RKSHLVGKNH LRITADYYRN KARDIINKHN HKRRHIGKRG RKERENSSQN ETLKVTCLSN KEKRHIMHV KKMNQKELAQ TSIDTLKLLY DGSPGYSKVF VDANRFDIGD LVKASKLPQR ANEKSAHHSF KQTSRSRDET C ESNPFPRL ...String:
MTRYYCEYCH SYLTHDTLSV RKSHLVGKNH LRITADYYRN KARDIINKHN HKRRHIGKRG RKERENSSQN ETLKVTCLSN KEKRHIMHV KKMNQKELAQ TSIDTLKLLY DGSPGYSKVF VDANRFDIGD LVKASKLPQR ANEKSAHHSF KQTSRSRDET C ESNPFPRL NNPKKLEPPK ILSQWSNTIP KTSIFYSVDI LQTTIKESKK RMHSDGIRKP SSANGYKRRR YGN

UniProtKB: U1 small nuclear ribonucleoprotein C

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Macromolecule #3: U1 small nuclear ribonucleoprotein A

MacromoleculeName: U1 small nuclear ribonucleoprotein A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 40.413961 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
SequenceString: MSALYFQNLP SRPANKENYT RLLLKHINPN NKYAINPSLP LPHNKLQISS QPLMLLDDQM GLLEVSISRS SKMTNQAFLT FVTQEEADR FLEKYTTTAL KVQGRKVRMG KARTNSLLGL SIEMQKKKGN DETYNLDIKK VLKARKLKRK LRSDDICAKK F RLKRQIRR ...String:
MSALYFQNLP SRPANKENYT RLLLKHINPN NKYAINPSLP LPHNKLQISS QPLMLLDDQM GLLEVSISRS SKMTNQAFLT FVTQEEADR FLEKYTTTAL KVQGRKVRMG KARTNSLLGL SIEMQKKKGN DETYNLDIKK VLKARKLKRK LRSDDICAKK F RLKRQIRR LKHKLRSRKV EEAEIDRIVK EFETRRLENM KSQQENLKQS QKPLKRAKVS NTMENPPNKV LLIQNLPSGT TE QLLSQIL GNEALVEIRL VSVRNLAFVE YETVADATKI KNQLGSTYKL QNNDVTIGFA KGRRIPGLIN PWKRRWKKNF IAV SAANRF KKISSSGALD YDIPTTASEN LYFQ

UniProtKB: U1 small nuclear ribonucleoprotein A

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Macromolecule #4: U1 small nuclear ribonucleoprotein component PRP42

MacromoleculeName: U1 small nuclear ribonucleoprotein component PRP42 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 65.22202 KDa
SequenceString: MDKYTALIHD ENFSTLTLNV SRYPKSLAYW EKLLNYIVKA SAPICKSTEP QLLKLIRCTY SSMLNEFPYL ENYYIDFALL EYKLGNVSM SHKIFQRGLQ AFNQRSLLLW TSYLKFCNNV ISHQKQLFKK YETAEEYVGL HFFSGEFWDL YLEQISSRCT S SKKYWNVL ...String:
MDKYTALIHD ENFSTLTLNV SRYPKSLAYW EKLLNYIVKA SAPICKSTEP QLLKLIRCTY SSMLNEFPYL ENYYIDFALL EYKLGNVSM SHKIFQRGLQ AFNQRSLLLW TSYLKFCNNV ISHQKQLFKK YETAEEYVGL HFFSGEFWDL YLEQISSRCT S SKKYWNVL RKILEIPLHS FSKFYALWLQ RIDDIMDLKQ LSQLTSKDEL LKKLKIDINY SGRKGPYLQD AKKKLKKITK EM YMVVQYQ VLEIYSIFES KIYINYYTSP ETLVSSDEIE TWIKYLDYTI TLQTDSLTHL NFQRALLPLA HYDLVWIKYS KWL INSKND LLGAKNVLLM GLKFSLKKTE IIKLLYSVIC KLNEYVLLRN LLEKIESSYS DNVENVDDFE IFWDYLQFKT FCQN SLYSS RYSDSQSNGL LNKELFDKVW KRLSCKEKKS GQEILLNNLV QFYSKDTVEF VEKNIFQKII EFGWEYYLQN GMFWN CYCR LIYFDTSRSY LDKRQYIVRK IWPQIDKKFA QSVLPSLTEF CESYFPEEMD TLEEMFTEEP

UniProtKB: U1 small nuclear ribonucleoprotein component PRP42

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Macromolecule #5: Pre-mRNA-processing factor 39

MacromoleculeName: Pre-mRNA-processing factor 39 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 74.834742 KDa
SequenceString: MPDETNFTIE DIEPRPDALR GLDTQFLQDN TALVQAYRGL DWSDISSLTQ MVDVIEQTVV KYGNPNDSIK LALETILWQI LRKYPLLFG FWKRFATIEY QLFGLKKSIA VLATSVKWFP TSLELWCDYL NVLCVNNPNE TDFIRNNFEI AKDLIGKQFL S HPFWDKFI ...String:
MPDETNFTIE DIEPRPDALR GLDTQFLQDN TALVQAYRGL DWSDISSLTQ MVDVIEQTVV KYGNPNDSIK LALETILWQI LRKYPLLFG FWKRFATIEY QLFGLKKSIA VLATSVKWFP TSLELWCDYL NVLCVNNPNE TDFIRNNFEI AKDLIGKQFL S HPFWDKFI EFEVGQKNWH NVQRIYEYII EVPLHQYARF FTSYKKFLNE KNLKTTRNID IVLRKTQTTV NEIWQFESKI KQ PFFNLGQ VLNDDLENWS RYLKFVTDPS KSLDKEFVMS VFDRCLIPCL YHENTWMMYI KWLTKKNISD EVVVDIYQKA NTF LPLDFK TLRYDFLRFL KRKYRSNNTL FNNIFNETVS RYLKIWPNDI LLMTEYLCML KRHSFKNSLD QSPKEILEKQ TSFT KILET SITNYINNQI DAKVHLQTLI NDKNLSIVVV ELIKTTWLVL KNNMQTRKYF NLYQKNILIK NSVPFWLTYY KFEKS NVNF TKLNKFIREL GVEIYLPTTV MNDILTDYKT FYLTHSNIVT YESSIIDSNT FDPILYPELK MSNPKYDPVL NTTANV DWH KKTEWKEAGH IGITTERPQI SNSIIECNSG TLIQKPISLP NFRNLEKINQ VKINDLYTEE FLKEGK

UniProtKB: Pre-mRNA-processing factor 39

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Macromolecule #6: Protein NAM8

MacromoleculeName: Protein NAM8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.01084 KDa
SequenceString: MSYKQTTYYP SRGNLVRNDS SPYTNTISSE TNNSSTSVLS LQGASNVSLG TTGNQLYMGD LDPTWDKNTV RQIWASLGEA NINVRMMWN NTLNNGSRSS MGPKNNQGYC FVDFPSSTHA ANALLKNGML IPNFPNKKLK LNWATSSYSN SNNSLNNVKS G NNCSIFVG ...String:
MSYKQTTYYP SRGNLVRNDS SPYTNTISSE TNNSSTSVLS LQGASNVSLG TTGNQLYMGD LDPTWDKNTV RQIWASLGEA NINVRMMWN NTLNNGSRSS MGPKNNQGYC FVDFPSSTHA ANALLKNGML IPNFPNKKLK LNWATSSYSN SNNSLNNVKS G NNCSIFVG DLAPNVTESQ LFELFINRYA STSHAKIVHD QVTGMSKGYG FVKFTNSDEQ QLALSEMQGV FLNGRAIKVG PT SGQQQHV SGNNDYNRSS SSLNNENVDS RFLSKGQSFL SNGNNNMGFK RNHMSQFIYP VQQQPSLNHF TDPNNTTVFI GGL SSLVTE DELRAYFQPF GTIVYVKIPV GKCCGFVQYV DRLSAEAAIA GMQGFPIANS RVRLSWGRSA KQTALLQQAM LSNS LQVQQ QQPGLQQPNY GYIPSSTCEA PVLPDNNVSS TMLPGCQILN YSNPYANANG LGSNNFSFYS NNNATNTQAT SLLAD TSSM DLSGTGGQQV IMQGSEAVVN STNAMLNRLE QGSNGFMFA

UniProtKB: Protein NAM8

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Macromolecule #7: 56 kDa U1 small nuclear ribonucleoprotein component

MacromoleculeName: 56 kDa U1 small nuclear ribonucleoprotein component / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 56.575277 KDa
SequenceString: MRPRRRGLAY HHTKPKGQLS QGHYPTTSND GQRRKVGNSE AFQSFDIWKN LDRIRSTKKN AGQFIKGSLL ILPMRTEDKQ QFDECMDEL HKYISKDILR CYPQKEQKDE GMLFYIVLKD FNILDSCFVL SVLLAFQKRL WMAPSEKSYF RVPKNINLTG S FYLPKNIE ...String:
MRPRRRGLAY HHTKPKGQLS QGHYPTTSND GQRRKVGNSE AFQSFDIWKN LDRIRSTKKN AGQFIKGSLL ILPMRTEDKQ QFDECMDEL HKYISKDILR CYPQKEQKDE GMLFYIVLKD FNILDSCFVL SVLLAFQKRL WMAPSEKSYF RVPKNINLTG S FYLPKNIE TGRGHIITSY RREQPSSSIV EVGFNVVPDF QQFQVKACHV SKFMNELSNF FSQVEFGKCE ANVINYFKRE YN RTYSQIS LALYELPLIG DGLFDIKSYI SKTRPIIETS KAQMIKHISE MKAYNEISGL QGDQFPRQQR PLSNSPSSNS ISS SQTIEA GATSYQTQPQ RHAVNKPSNV LNSSNRHSGP KTFEDGRYSE GNKPGFMTQD EIKQHCIGTI KASMDAVKKK SSYQ ILKTY VRCPRQNYID IVYQNLNDLR SKTNCNIVVL NLNNLHESQM WLESLNTTNY TIFAQAPHPS TIRVISIGGV GEYIV KALE LILNILEH

UniProtKB: 56 kDa U1 small nuclear ribonucleoprotein component

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Macromolecule #8: U1 small nuclear ribonucleoprotein component SNU71,U1 small nucle...

MacromoleculeName: U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.48532 KDa
SequenceString: MRDIVFVSPQ LYLSSQEGWK SDSAKSGFIP ILKNDLQRFQ DSLKHIVDAR NS(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
MRDIVFVSPQ LYLSSQEGWK SDSAKSGFIP ILKNDLQRFQ DSLKHIVDAR NS(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: U1 small nuclear ribonucleoprotein component SNU71

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Macromolecule #9: Protein LUC7

MacromoleculeName: Protein LUC7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.245885 KDa
SequenceString: MSTMSTPAAE QRKLVEQLMG RDFSFRHNRY SHQKRDLGLH DPKICKSYLV GECPYDLFQG TKQSLGKCPQ MHLTKHKIQY EREVKQGKT FPEFEREYLA ILSRFVNECN GQISVALQNL KHTAEERMKI QQVTEELDVL DVRIGLMGQE IDSLIRADEV S MGMLQSVK ...String:
MSTMSTPAAE QRKLVEQLMG RDFSFRHNRY SHQKRDLGLH DPKICKSYLV GECPYDLFQG TKQSLGKCPQ MHLTKHKIQY EREVKQGKT FPEFEREYLA ILSRFVNECN GQISVALQNL KHTAEERMKI QQVTEELDVL DVRIGLMGQE IDSLIRADEV S MGMLQSVK LQELISKRKE VAKRVRNITE NVGQSAQQKL QVCEVCGAYL SRLDTDRRLA DHFLGKIHLG YVKMREDYDR LM KNNRTTN ASKTATTLPG RRFV

UniProtKB: Protein LUC7

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Macromolecule #10: Pre-mRNA-processing protein PRP40

MacromoleculeName: Pre-mRNA-processing protein PRP40 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 69.176016 KDa
SequenceString: MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELISQEELLL RENGWKAAKT ADGKVYYYNP TTRETSWTIP AFEKKVEPIA EQKHDTVSH AQVNGNRIAL TAGEKQEPGR TINEEESQYA NNSKLLNVRR RTKEEAEKEF ITMLKENQVD STWSFSRIIS E LGTRDPRY ...String:
MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELISQEELLL RENGWKAAKT ADGKVYYYNP TTRETSWTIP AFEKKVEPIA EQKHDTVSH AQVNGNRIAL TAGEKQEPGR TINEEESQYA NNSKLLNVRR RTKEEAEKEF ITMLKENQVD STWSFSRIIS E LGTRDPRY WMVDDDPLWK KEMFEKYLSN RSADQLLKEH NETSKFKEAF QKMLQNNSHI KYYTRWPTAK RLIADEPIYK HS VVNEKTK RQTFQDYIDT LIDTQKESKK KLKTQALKEL REYLNGIITT SSSETFITWQ QLLNHYVFDK SKRYMANRHF KVL THEDVL NEYLKIVNTI ENDLQNKLNE LRLRNYTRDR IARDNFKSLL REVPIKIKAN TRWSDIYPHI KSDPRFLHML GRNG SSCLD LFLDFVDEQR MYIFAQRSIA QQTLIDQNFE WNDADSDEIT KQNIEKVLEN DRKFDKVDKE DISLIVDGLI KQRNE KIQQ KLQNERRILE QKKHYFWLLL QRTYTKTGKP KPSTWDLASK ELGESLEYKA LGDEDNIRRQ IFEDFKPESS APTAES ATA NLTLTASKKR HLTPAVELDY

UniProtKB: Pre-mRNA-processing protein PRP40

+
Macromolecule #11: Small nuclear ribonucleoprotein-associated protein B

MacromoleculeName: Small nuclear ribonucleoprotein-associated protein B / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.42699 KDa
SequenceString: MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK LRPRKDSKDG TTLNIKVEKR VLGLTILRG EQILSTVVED KPLLSKKERL VRDKKEKKQA QKQTKLRKEK EKKPGKIAKP NTANAKHTSS NSREIAQPSS S RYNGGNDN ...String:
MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK LRPRKDSKDG TTLNIKVEKR VLGLTILRG EQILSTVVED KPLLSKKERL VRDKKEKKQA QKQTKLRKEK EKKPGKIAKP NTANAKHTSS NSREIAQPSS S RYNGGNDN IGANRSRFNN EAPPQTRKFQ PPPGFKRK

UniProtKB: Small nuclear ribonucleoprotein-associated protein B

+
Macromolecule #12: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.296798 KDa
SequenceString:
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP RLNKLNSNGI AMASLYLTGG QQPTASDNIA SLQYINIRG NTIRQIILPD SLNLDSLLVD QKQLNSLRRS GQIANDPSKK RRRDFGAPAN KRPRRGL

UniProtKB: Small nuclear ribonucleoprotein Sm D1

+
Macromolecule #13: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 12.876066 KDa
SequenceString:
MSSQIIDRPK HELSRAELEE LEEFEFKHGP MSLINDAMVT RTPVIISLRN NHKIIARVKA FDRHCNMVLE NVKELWTEKK GKNVINRER FISKLFLRGD SVIVVLKTPV E

UniProtKB: Small nuclear ribonucleoprotein Sm D2

+
Macromolecule #14: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.240139 KDa
SequenceString:
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSS RPMPPIRGPK RR

UniProtKB: Small nuclear ribonucleoprotein Sm D3

+
Macromolecule #15: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.385098 KDa
SequenceString:
MSNKVKTKAM VPPINCIFNF LQQQTPVTIW LFEQIGIRIK GKIVGFDEFM NVVIDEAVEI PVNSADGKED VEKGTPLGKI LLKGDNITL ITSAD

UniProtKB: Small nuclear ribonucleoprotein E

+
Macromolecule #16: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 9.669945 KDa
SequenceString:
MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV AGVSHGTLGE IFIRCNNVLY IRELPN

UniProtKB: Small nuclear ribonucleoprotein F

+
Macromolecule #17: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.490809 KDa
SequenceString:
MVSTPELKKY MDKKILLNIN GSRKVAGILR GYDIFLNVVL DDAMEINGED PANNHQLGLQ TVIRGNSIIS LEALDAI

UniProtKB: Small nuclear ribonucleoprotein G

+
Macromolecule #20: Nuclear cap-binding protein complex subunit 1

MacromoleculeName: Nuclear cap-binding protein complex subunit 1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.115047 KDa
SequenceString: MFNRKRRGDF DEDENYRDFR PRMPKRQRIP PVVQLCKEMM PDIRTIGESV KAFEDDIKFL SEAIMNEYGH EDYFNNALLS TLNAVVVEQ PQKQAAIALL TMVVNSKNNV AGKSIINYFF EELQKWCKQT YNDEFKSTSN ETGPWNKIKL ILRFLSILSP M FLVDELIN ...String:
MFNRKRRGDF DEDENYRDFR PRMPKRQRIP PVVQLCKEMM PDIRTIGESV KAFEDDIKFL SEAIMNEYGH EDYFNNALLS TLNAVVVEQ PQKQAAIALL TMVVNSKNNV AGKSIINYFF EELQKWCKQT YNDEFKSTSN ETGPWNKIKL ILRFLSILSP M FLVDELIN IYKSLFELSI ELNNLDPGNR VPLSEAIYTN TLLNIPYLFF FNRNNDGLRT KVEELLAYVE QNYLVKTTDI NL LREYNGE PPYEMVELVR VVLPNVKKAL INNLEQLNEL FPDWNHLLTP QTGDEGFNDA LTLPSVDDLK SFVRLNKNFG SVD SMWKTP RYAFHVYLPN SAGNFETVVP ISTYAGQLFN DIIIDLVESL EFNRKEVARQ VITLDLFFKA GIFTEPGESI AQLI ATYEE NPLAPTFKIE DLAIETILGL IFKLPSVSQP FAYFYTLLVD ICQNSPKAIA PVFGRAFRFF YSHLDSLDFE LKLRY LDWF SIQMSNFNFS WKWNEWEDDS IKFGKYFYNP KVNFAKNLIQ KELRLTSNFS EVEDSLPQEF TKYLDTSYIP RDQLIN YYQ SLFTGYTVEE DSVRKNDLYF RQEGVPMENT VRKILDYTHK ANNSREVTEL ESILGELKNE YGSIISDFNR FVIILLV QA VTDSGSRSLS HANKYINDLK EDLKTIFAKI ELDIETKEYI IIEAVLTFWN ANPQTGFLVA DAFKYAGLLT SRTIFTFI F NETGLKNNGL IEATAIEAVF RNLSQQISEE NESGNNFEFV FERLCTIANS TIDLLDVNAD EDIEIPKVNG EMDIDDIED DKLDLKWKYF TVIGFIKSIL RRYSHEYREL ADKFIANIDN AIPHESTRRT ISNWIQETKE V

UniProtKB: Nuclear cap-binding protein complex subunit 1

+
Macromolecule #21: Nuclear cap-binding protein subunit 2

MacromoleculeName: Nuclear cap-binding protein subunit 2 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 23.803467 KDa
SequenceString: MSLEEFDEVK YDHSTKRLDT PSRYLLRKAR RNPNGLQELR ESMKSSTIYV GNLSFYTSEE QIYELFSKCG TIKRIIMGLD RFKFTPCGF CFIIYSCPDE ALNALKYLSD TKLDEKTITI DLDPGFEDGR QFGRGKSGGQ VSDELRFDFD ASRGGFAIPF A ERVGVPHS ...String:
MSLEEFDEVK YDHSTKRLDT PSRYLLRKAR RNPNGLQELR ESMKSSTIYV GNLSFYTSEE QIYELFSKCG TIKRIIMGLD RFKFTPCGF CFIIYSCPDE ALNALKYLSD TKLDEKTITI DLDPGFEDGR QFGRGKSGGQ VSDELRFDFD ASRGGFAIPF A ERVGVPHS RFDNSSSQSN TNNYIPPPDA MGTFRPGFDE EREDDNYVPQ

UniProtKB: Nuclear cap-binding protein subunit 2

+
Macromolecule #18: U1 snRNA

MacromoleculeName: U1 snRNA / type: rna / ID: 18 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 182.114516 KDa
SequenceString: AUACUUACCU UAAGAUAUCA GAGGAGAUCA AGAAGUCCUA CUGAUCAAAC AUGCGCUUCC AAUAGUAGAA GGACGUUAAG CAUUUAUCA UUGAACUAUA AUUGUUCAUU GAAGUCAUUG AUGCAAACUC CUUGGUCACA CACACAUACG GCGCGGAAGG C GUGUUUGC ...String:
AUACUUACCU UAAGAUAUCA GAGGAGAUCA AGAAGUCCUA CUGAUCAAAC AUGCGCUUCC AAUAGUAGAA GGACGUUAAG CAUUUAUCA UUGAACUAUA AUUGUUCAUU GAAGUCAUUG AUGCAAACUC CUUGGUCACA CACACAUACG GCGCGGAAGG C GUGUUUGC UGACGUUUCC AUUCCCUUGU UUCAAUCAUU GGUUAAUCCC UUGAUUCCUU UGGGGAUUUU UGGGUUAAAC UG AUUUUUG GGGCCCUUUG UUUCUUCUGC CUGGAGAAGU UUGACACCAA AUUCAAAUUG GUGUUAGGGG AGCUGGGGCC UUU CAAAAG AGAGCUUUGU AGAGGCAUUC UUUUUGACUA CUUUUCUCUA GCGUGCCAUU UUAGUUUUUG ACGGCAGAUU CGAA UGAAC UUAAGUUUAU GAUGAAGGUA UGGCUGUUGA GAUUAUUUGG UCGGGAUUGU AGUUUGAAGA UGUGCUCUUU UGAGC AGUC UCAACUUUGC UCGUUCCCGU UAUGGGAAAA AUUUUGGAAG GUCUUGGUAG GAACGGGUGG AUCUUAUAAU UUUUGA UUU AUUUU

GENBANK: GENBANK: CP008198.1

+
Macromolecule #19: UBC4 pre-mRNA

MacromoleculeName: UBC4 pre-mRNA / type: rna / ID: 19 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 81.030773 KDa
SequenceString: GGGAACUAAG UGAUCUAGAA AGGUAUGUCU AAAGUUAUGG CCACGUUUCA AAUGCGUGCU UUUUUUUUAA AACUUAUGCU CUUAUUUAC UAACAAAAUC AACAUGCUAU UGAACUAGAG AUCCACCUAC UUCAUGUUCA GCCGGUCCAG GAUCCGAUAU C CGUACACC ...String:
GGGAACUAAG UGAUCUAGAA AGGUAUGUCU AAAGUUAUGG CCACGUUUCA AAUGCGUGCU UUUUUUUUAA AACUUAUGCU CUUAUUUAC UAACAAAAUC AACAUGCUAU UGAACUAGAG AUCCACCUAC UUCAUGUUCA GCCGGUCCAG GAUCCGAUAU C CGUACACC AUCAGGGUAC GAGCUAGCCC AUGGCGUACA CCAUCAGGGU ACGACUAGUA GAUCUCGUAC ACCAUCAGGG UA CGGAAUU CUCUAG

+
Macromolecule #22: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 22 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 124825
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

+
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