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- EMDB-8622: S. cerevisiae U1 snRNP -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-8622
TitleS. cerevisiae U1 snRNP
Map dataS. cerevisiae U1 snRNP
Sample
  • Complex: S. cerevisiae U1 snRNP
    • Protein or peptide: x 15 types
    • RNA: x 1 types
Function / homology
Function and homology information


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 ...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 / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / : / Sm domain profile. / LSM domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
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 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 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi X / Liu S / Jiang J / Zhang L / Espinosa S / Hill RC / Hansen KC / Zhou ZH / Zhao R
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM114178 United States
National Institutes of Health/National Institute of General Medical SciencesGM071940 United States
National Institutes of Health/National Institute of General Medical SciencesGM114178-02S2 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI094386 United States
CitationJournal: Nat Commun / Year: 2017
Title: CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing.
Authors: Xueni Li / Shiheng Liu / Jiansen Jiang / Lingdi Zhang / Sara Espinosa / Ryan C Hill / Kirk C Hansen / Z Hong Zhou / Rui Zhao /
Abstract: U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for ...U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs are stable components of U1 snRNP. Here, we report the cryoEM structure of yeast U1 snRNP at 3.6 Å resolution with atomic models for ten core proteins, nearly all essential domains of its RNA, and five stably associated auxiliary proteins. The foot-shaped yeast U1 snRNP contains a core in the "ball-and-toes" region architecturally similar to the human U1 snRNP. All auxiliary proteins are in the "arch-and-heel" region and connected to the core through the Prp42/Prp39 paralogs. Our demonstration that homodimeric human PrpF39 directly interacts with U1C-CTD, mirroring yeast Prp42/Prp39, supports yeast U1 snRNP as a model for understanding how transiently associated auxiliary proteins recruit human U1 snRNP in alternative splicing.
History
DepositionFeb 24, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseNov 15, 2017-
UpdateJul 24, 2019-
Current statusJul 24, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n7x
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8622.png

Downloads & links

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Map

FileDownload / File: emd_8622.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS. cerevisiae U1 snRNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 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: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.2127786 - 0.34284478
Average (Standard dev.)-0.00002665508 (±0.007038105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2130.343-0.000

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Supplemental data

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Sample components

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Entire : S. cerevisiae U1 snRNP

EntireName: S. cerevisiae U1 snRNP
Components
  • Complex: S. cerevisiae U1 snRNP
    • 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,TAP tag
    • 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: Protein LUC7
    • 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: RNA

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Supramolecule #1: S. cerevisiae U1 snRNP

SupramoleculeName: S. cerevisiae U1 snRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Baker's yeast (brewer's 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

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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: Baker's yeast (brewer's 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

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Macromolecule #3: U1 small nuclear ribonucleoprotein A,TAP tag

MacromoleculeName: U1 small nuclear ribonucleoprotein A,TAP tag / type: protein_or_peptide / ID: 3 / Details: C-terminal TAP tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 55.59248 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's 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 LYFQGEFGLA QHDEAVDNKF NKEQQNAFYE ILHLPNLNEE QRNAFIQSLK DDPS QSANL LAEAKKLNDA QAPKVDNKFN KEQQNAFYEI LHLPNLNEEQ RNAFIQSLKD DPSQSANLLA EAKKLNDAQA PKVDA NHQZ

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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: Baker's yeast (brewer's 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

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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: Baker's yeast (brewer's 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

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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: Baker's yeast (brewer's 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

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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: Baker's yeast (brewer's 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

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Macromolecule #8: Protein LUC7

MacromoleculeName: Protein LUC7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's 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

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Macromolecule #9: Small nuclear ribonucleoprotein-associated protein B

MacromoleculeName: Small nuclear ribonucleoprotein-associated protein B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's 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

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Macromolecule #10: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's 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

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Macromolecule #11: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 12.876066 KDa
SequenceString:
MSSQIIDRPK HELSRAELEE LEEFEFKHGP MSLINDAMVT RTPVIISLRN NHKIIARVKA FDRHCNMVLE NVKELWTEKK GKNVINRER FISKLFLRGD SVIVVLKTPV E

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Macromolecule #12: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.240139 KDa
SequenceString:
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSS RPMPPIRGPK RR

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Macromolecule #13: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.385098 KDa
SequenceString:
MSNKVKTKAM VPPINCIFNF LQQQTPVTIW LFEQIGIRIK GKIVGFDEFM NVVIDEAVEI PVNSADGKED VEKGTPLGKI LLKGDNITL ITSAD

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Macromolecule #14: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 9.669945 KDa
SequenceString:
MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV AGVSHGTLGE IFIRCNNVLY IRELPN

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Macromolecule #15: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.490809 KDa
SequenceString:
MVSTPELKKY MDKKILLNIN GSRKVAGILR GYDIFLNVVL DDAMEINGED PANNHQLGLQ TVIRGNSIIS LEALDAI

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Macromolecule #16: RNA

MacromoleculeName: RNA / type: rna / ID: 16 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 352900

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6n7x:
S. cerevisiae U1 snRNP

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