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- EMDB-6973: Cryo-EM structure of the yeast pre-B complex at an average resolu... -

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Basic information

Entry
Database: EMDB / ID: EMD-6973
TitleCryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)
Map dataU1 snRNP region of the spliceosomal pre-B complex
Sample
  • Cell: Pre-B spliceosomal complex
    • RNA: x 2 types
    • Protein or peptide: x 18 types
  • Ligand: x 1 types
Keywordsspliceosme / assemply / pre-B complex / U1 snRNP / Splicing
Function / homology
Function and homology information


first spliceosomal transesterification activity / positive regulation of RNA binding / splicing factor binding / mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex ...first spliceosomal transesterification activity / positive regulation of RNA binding / splicing factor binding / mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / pre-mRNA 5'-splice site binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP 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 / U1 small nuclear ribonucleoprotein C / 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 / PWI domain ...Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein C / 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 / PWI domain / PWI, domain in splicing factors / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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 / : / DEAD-box subfamily ATP-dependent helicases signature. / Sm domain profile. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / LSM domain superfamily / Zinc finger C2H2 superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / U1 small nuclear ribonucleoprotein A / 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 ...Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / U1 small nuclear ribonucleoprotein A / 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 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBai R / Wan R
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31430020 China
National Natural Science Foundation of China31621092 China
Ministry of Science and Technology (China)2016YFA0501100 China
CitationJournal: Science / Year: 2018
Title: Structures of the fully assembled spliceosome before activation.
Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Jianlin Lei / Yigong Shi /
Abstract: The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 ...The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
History
DepositionMay 16, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseAug 29, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zwn
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6973.png

Downloads & links

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Map

FileDownload / File: emd_6973.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationU1 snRNP region of the spliceosomal pre-B complex
Voxel sizeX=Y=Z: 1.338 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.19564165 - 0.34690544
Average (Standard dev.)0.00067012367 (±0.009224686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 535.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z535.200535.200535.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1960.3470.001

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Supplemental data

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Sample components

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Entire : Pre-B spliceosomal complex

EntireName: Pre-B spliceosomal complex
Components
  • Cell: Pre-B spliceosomal complex
    • RNA: pre-mRNAPrimary transcript
    • RNA: U1 snRNAU1 spliceosomal RNA
    • 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: 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
    • Protein or peptide: U1 small nuclear ribonucleoprotein component SNU71
    • Protein or peptide: Protein LUC7
    • Protein or peptide: U1 snRNP
    • Protein or peptide: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
  • Ligand: ZINC ION

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Supramolecule #1: Pre-B spliceosomal complex

SupramoleculeName: Pre-B spliceosomal complex / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: pre-mRNA

MacromoleculeName: pre-mRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 7.130372 KDa
SequenceString:
AAAAAAAAAA GGUAUGUAUU AA

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Macromolecule #2: U1 snRNA

MacromoleculeName: U1 snRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
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

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Macromolecule #3: U1 small nuclear ribonucleoprotein 70 kDa homolog

MacromoleculeName: U1 small nuclear ribonucleoprotein 70 kDa homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #4: U1 small nuclear ribonucleoprotein C

MacromoleculeName: U1 small nuclear ribonucleoprotein C / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #5: U1 small nuclear ribonucleoprotein A

MacromoleculeName: U1 small nuclear ribonucleoprotein A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 34.438105 KDa
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 K

UniProtKB: U1 small nuclear ribonucleoprotein A

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Macromolecule #6: U1 small nuclear ribonucleoprotein component PRP42

MacromoleculeName: U1 small nuclear ribonucleoprotein component PRP42 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #7: Pre-mRNA-processing factor 39

MacromoleculeName: Pre-mRNA-processing factor 39 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #8: Protein NAM8

MacromoleculeName: Protein NAM8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #9: 56 kDa U1 small nuclear ribonucleoprotein component

MacromoleculeName: 56 kDa U1 small nuclear ribonucleoprotein component / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #10: Small nuclear ribonucleoprotein-associated protein B

MacromoleculeName: Small nuclear ribonucleoprotein-associated protein B / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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

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Macromolecule #11: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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

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Macromolecule #12: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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

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Macromolecule #13: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 11.240139 KDa
SequenceString:
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSS RPMPPIRGPK RR

UniProtKB: Small nuclear ribonucleoprotein Sm D3

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Macromolecule #14: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 10.385098 KDa
SequenceString:
MSNKVKTKAM VPPINCIFNF LQQQTPVTIW LFEQIGIRIK GKIVGFDEFM NVVIDEAVEI PVNSADGKED VEKGTPLGKI LLKGDNITL ITSAD

UniProtKB: Small nuclear ribonucleoprotein E

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Macromolecule #15: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 9.669945 KDa
SequenceString:
MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV AGVSHGTLGE IFIRCNNVLY IRELPN

UniProtKB: Small nuclear ribonucleoprotein F

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Macromolecule #16: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 8.490809 KDa
SequenceString:
MVSTPELKKY MDKKILLNIN GSRKVAGILR GYDIFLNVVL DDAMEINGED PANNHQLGLQ TVIRGNSIIS LEALDAI

UniProtKB: Small nuclear ribonucleoprotein G

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Macromolecule #17: U1 small nuclear ribonucleoprotein component SNU71

MacromoleculeName: U1 small nuclear ribonucleoprotein component SNU71 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 71.383453 KDa
SequenceString: MRDIVFVSPQ LYLSSQEGWK SDSAKSGFIP ILKNDLQRFQ DSLKHIVDAR NSLSETLLNS NDDGSIHNSD QNTGLNKDKE ASIADNNSA NKCATSSSRY QELKQFLPIS LDQQIHTVSL QGVSSSFSRG QIESLLDHCL NLALTETQSN SALKVEAWSS F SSFLDTQD ...String:
MRDIVFVSPQ LYLSSQEGWK SDSAKSGFIP ILKNDLQRFQ DSLKHIVDAR NSLSETLLNS NDDGSIHNSD QNTGLNKDKE ASIADNNSA NKCATSSSRY QELKQFLPIS LDQQIHTVSL QGVSSSFSRG QIESLLDHCL NLALTETQSN SALKVEAWSS F SSFLDTQD IFIRFSKVDE DEAFVNTLNY CKALFAFIRK LHEDFKIELH LDLNTKEYVE DRTGTIPSVK PEKASEFYSV FK NIEDQTD ERNSKKEQLD DSSTQYKVDT NTLSDLPSDA LDQLCKDIIE FRTKVVSIEK EKKMKSTYEE SRRQRHQMQK VFD QIRKNH SGAKGSANTE EEDTNMEDED EEDDTEDDLA LEKRKEERDL EESNRRYEDM LHQLHSNTEP KIKSIRADIM SAEN YEEHL EKNRSLYLKE LLHLANDVHY DHHRSFKEQE ERRDEEDRAK NGNAKELAPI QLSDGKAISA GKAAAITLPE GTVKS ENYN ADKNVSESSE HVKIKFDFKK AIDHSVESSS EDEGYRESEL PPTKPSERSA AEDRLPFTAD ELNIRLTNLK ESRYVD ELV REFLGVYEDE LVEYILENIR VNQSKQALLN ELRETFDEDG ETIADRLWSR KEFRLG

UniProtKB: U1 small nuclear ribonucleoprotein component SNU71

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Macromolecule #18: Protein LUC7

MacromoleculeName: Protein LUC7 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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 #19: U1 snRNP

MacromoleculeName: U1 snRNP / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 3.500827 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAA

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Macromolecule #20: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28

MacromoleculeName: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 66.733188 KDa
SequenceString: MARPIDVSQL IAGINKKKGL DENTSGKISK PRFLNKQERS KQERLKENEE SLTPTQSDSA KVEIKKVNSR DDSFFNETND KKRNPSKQN GSKFHFSWNE SEDTLSGYDP IVSTRAIDLL WKGKTPKNAA ESSYMGKHWT EKSLHEMNER DWRILKEDYA I VTKGGTVE ...String:
MARPIDVSQL IAGINKKKGL DENTSGKISK PRFLNKQERS KQERLKENEE SLTPTQSDSA KVEIKKVNSR DDSFFNETND KKRNPSKQN GSKFHFSWNE SEDTLSGYDP IVSTRAIDLL WKGKTPKNAA ESSYMGKHWT EKSLHEMNER DWRILKEDYA I VTKGGTVE NPLRNWEELN IIPRDLLRVI IQELRFPSPT PIQRITIPNV CNMKQYRDFL GVASTGSGKT LAFVIPILIK MS RSPPRPP SLKIIDGPKA LILAPTRELV QQIQKETQKV TKIWSKESNY DCKVISIVGG HSLEEISFSL SEGCDILVAT PGR LIDSLE NHLLVMKQVE TLVLDEADKM IDLGFEDQVT NILTKVDINA DSAVNRQTLM FTATMTPVIE KIAAGYMQKP VYAT IGVET GSEPLIQQVV EYADNDEDKF KKLKPIVAKY DPPIIIFINY KQTADWLAEK FQKETNMKVT ILHGSKSQEQ REHSL QLFR TNKVQIMIAT NVAARGLDIP NVSLVVNFQI SKKMDDYIHR IGRTGRAANE GTAVSFVSAA EDESLIRELY KYVRKH DPL NSNIFSEAVK NKYNVGKQLS NEIIY

UniProtKB: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 500657

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