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- EMDB-8008: Combined Body and arm regions of the yeast spliceosomal U4/U6.U5 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8008
TitleCombined Body and arm regions of the yeast spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 1
Map dataCombined Body and arm regions of the spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 1
Sample
  • Complex: tri-snRNP complex with 30 proteins and 3 snRNA
    • RNA: x 3 types
    • Protein or peptide: x 27 types
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsNguyen THD / Galej WP / Bai X-C / Oubridge C / Newman AJ / Scheres SHW / Nagai K
CitationJournal: Nature / Year: 2016
Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
History
DepositionDec 14, 2015-
Header (metadata) releaseJan 20, 2016-
Map releaseMar 30, 2016-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8008.png

Downloads & links

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Map

FileDownload / File: emd_8008.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined Body and arm regions of the spliceosomal U4/U6.U5 tri-snRNP by masked classification and refinement-Class 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 380 pix.
= 543.4 Å		1.43 Å/pix.
x 380 pix.
= 543.4 Å		1.43 Å/pix.
x 380 pix.
= 543.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.055081215 - 0.13692641
Average (Standard dev.)-0.00012243658 (±0.0040869545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 543.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z543.400543.400543.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0550.137-0.000

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Supplemental data

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Sample components

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Entire : tri-snRNP complex with 30 proteins and 3 snRNA

EntireName: tri-snRNP complex with 30 proteins and 3 snRNA
Components
  • Complex: tri-snRNP complex with 30 proteins and 3 snRNA
    • RNA: U4 snRNA
    • RNA: U6 snRNA
    • Protein or peptide: Prp8
    • Protein or peptide: Prp4
    • Protein or peptide: Prp6
    • Protein or peptide: Dib1
    • Protein or peptide: Prp31
    • Protein or peptide: Prp3
    • Protein or peptide: Brr2
    • Protein or peptide: unknown proteins
    • Protein or peptide: SmB
    • Protein or peptide: U4 SmD1
    • Protein or peptide: SmD2
    • Protein or peptide: SmD3
    • Protein or peptide: SmE
    • Protein or peptide: SmF
    • Protein or peptide: SmG
    • Protein or peptide: Snu66
    • Protein or peptide: U5 SmE
    • Protein or peptide: U5 SmD1
    • RNA: U5 snRNA
    • Protein or peptide: Snu13
    • Protein or peptide: LSm2
    • Protein or peptide: LSm3
    • Protein or peptide: LSm4
    • Protein or peptide: LSm5
    • Protein or peptide: LSm6
    • Protein or peptide: LSm7
    • Protein or peptide: LSm8
    • Protein or peptide: Snu114

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Supramolecule #1: tri-snRNP complex with 30 proteins and 3 snRNA

SupramoleculeName: tri-snRNP complex with 30 proteins and 3 snRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.5 MDa

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Macromolecule #1: U4 snRNA

MacromoleculeName: U4 snRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.813488 KDa
SequenceString:
AUCCUUAUGC ACGGGAAAU A CGCAUAUC AG UGAGGAU UCG UCCGAG AUUG UGUUU UUGCU GGUU GAAAUU UAA UUAUAAA CC AGACCGUC U CCUCAUGGU CAAUUCGGUG UUCGCUUUU G AAUACUUC AA GACUAUG UAG GGAAUU UUUG GAAUA CCUUU

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Macromolecule #2: U6 snRNA

MacromoleculeName: U6 snRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.635123 KDa
SequenceString:
GUUCGCGAAG UAACCCUUC G UGGACAUU UG GUCAAUU UGA AACAAU ACAG AGAUG AUCAG CAGU UCCCCU GCA UAAGGAU GA ACCGUUUU A CAAAGAGAU UUAUUUCGUU UU

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Macromolecule #21: U5 snRNA

MacromoleculeName: U5 snRNA / type: rna / ID: 21 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.305805 KDa
SequenceString: AAGCAGCUUU ACAGAUCAA U GGCGGAGG GA GGUCAAC AUC AAGAAC UGUG GGCCU UUUAU UGCC UAUAGA ACU UAUAACG AA CAUGGUUC U UGCCUUUUA CCAGAACCAU CCGGGUGUU G UCUCCAUA GA AACAGGU AAA GCUGUC CGUU ACUGU ...String:
AAGCAGCUUU ACAGAUCAA U GGCGGAGG GA GGUCAAC AUC AAGAAC UGUG GGCCU UUUAU UGCC UAUAGA ACU UAUAACG AA CAUGGUUC U UGCCUUUUA CCAGAACCAU CCGGGUGUU G UCUCCAUA GA AACAGGU AAA GCUGUC CGUU ACUGU GGGCU UGCC AUAUUU UUU GGAACUU UU CUGCCCUU U UUCUCAAUG AGUAAGGAGG GCGU

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Macromolecule #3: Prp8

MacromoleculeName: Prp8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 255.921422 KDa
SequenceString: MSGLPPPPPG FEEDSDLAL P PPPPPPPG YE IEELDNP MVP SSVNED TFLP PPPPP PSNFE INAE EIVDFT LPP PPPPPGL DE LETKAEKK V ELHGKRKLD IGKDTFVTRK SRKRAKKMT K KAKRSNLY TP KAEMPPE HLR KIINTH SDMA SKMYN ...String:
MSGLPPPPPG FEEDSDLAL P PPPPPPPG YE IEELDNP MVP SSVNED TFLP PPPPP PSNFE INAE EIVDFT LPP PPPPPGL DE LETKAEKK V ELHGKRKLD IGKDTFVTRK SRKRAKKMT K KAKRSNLY TP KAEMPPE HLR KIINTH SDMA SKMYN TDKKA FLGA LKYLPH AIL KLLENMP HP WEQAKEVK V LYHTSGAIT FVNETPRVIE PVYTAQWSA T WIAMRREK RD RTHFKRM RFP PFDDDE PPLS YEQHI ENIEP LDPI NLPLDS QDD EYVKDWL YD SRPLEEDS K KVNGTSYKK WSFDLPEMSN LYRLSTPLR D EVTDKNYY YL FDKKSFF NGK ALNNAI PGGP KFEPL YPREE EEDY NEFNSI DRV IFRVPIR SE YKVAFPHL Y NSRPRSVRI PWYNNPVSCI IQNDEEYDT P ALFFDPSL NP IPHFIDN NSS LNVSNT KENG DFTLP EDFAP LLAE EEELIL PNT KDAMSLY HS PFPFNRTK G KMVRAQDVA LAKKWFLQHP DEEYPVKVK V SYQKLLKN YV LNELHPT LPT NHNKTK LLKS LKNTK YFQQT TIDW VEAGLQ LCR QGHNMLN LL IHRKGLTY L HLDYNFNLK PTKTLTTKER KKSRLGNSF H LMRELLKM MK LIVDTHV QFR LGNVDA FQLA DGIHY ILNHI GQLT GIYRYK YKV MHQIRAC KD LKHIIYYK F NKNLGKGPG CGFWQPAWRV WLNFLRGTI P LLERYIGN LI TRQFEGR SNE IVKTTT KQRL DAYYD LELRN SVMD DILEMM PES IRQKKAR TI LQHLSEAW R CWKANIPWD VPGMPAPIKK IIERYIKSK A DAWVSAAH YN RERIKRG AHV EKTMVK KNLG RLTRL WIKNE QERQ RQIQKN GPE ITPEEAT TI FSVMVEWL E SRSFSPIPF PPLTYKNDTK ILVLALEDL K DVYASKVR LN ASEREEL ALI EEAYDN PHDT LNRIK KYLLT QRVF KPVDIT MME NYQNISP VY SVDPLEKI T DAYLDQYLW YEADQRKLFP NWIKPSDSE I PPLLVYKW TQ GINNLSE IWD VSRGQS AVLL ETTLG EMAEK IDFT LLNRLL RLI VDPNIAD YI TAKNNVVI N FKDMSHVNK YGLIRGLKFA SFIFQYYGL V IDLLLLGQ ER ATDLAGP ANN PNEFMQ FKSK EVEKA HPIRL YTRY LDRIYM LFH FEEDEGE EL TDEYLAEN P DPNFENSIG YNNRKCWPKD SRMRLIRQD V NLGRAVFW EI QSRVPTS LTS IKWENA FVSV YSKNN PNLLF SMCG FEVRIL PRQ RMEEVVS ND EGVWDLVD E RTKQRTAKA YLKVSEEEIK KFDSRIRGI L MASGSTTF TK VAAKWNT SLI SLFTYF REAI VATEP LLDIL VKGE TRIQNR VKL GLNSKMP TR FPPAVFYT P KELGGLGMI SASHILIPAS DLSWSKQTD T GITHFRAG MT HEDEKLI PTI FRYITT WENE FLDSQ RVWAE YATK RQEAIQ QNR RLAFEEL EG SWDRGIPR I STLFQRDRH TLAYDRGHRI RREFKQYSL E RNSPFWWT NS HHDGKLW NLN AYRTDV IQAL GGIET ILEHT LFKG TGFNSW EGL FWEKASG FE DSMQFKKL T HAQRTGLSQ IPNRRFTLWW SPTINRANV Y VGFLVQLD LT GIFLHGK IPT LKISLI QIFR AHLWQ KIHES IVFD ICQILD GEL DVLQIES VT KETVHPRK S YKMNSSAAD ITMESVHEWE VSKPSLLHE T NDSFKGLI TN KMWFDVQ LRY GDYDSH DISR YVRAK FLDYT TDNV SMYPSP TGV MIGIDLA YN MYDAYGNW F NGLKPLIQN SMRTIMKANP ALYVLRERI R KGLQIYQS SV QEPFLNS SNY AELFNN DIKL FVDDT NVYRV TVHK TFEGNV ATK AINGCIF TL NPKTGHLF L KIIHTSVWA GQKRLSQLAK WKTAEEVSA L VRSLPKEE QP KQIIVTR KAM LDPLEV HMLD FPNIA IRPTE LRLP FSAAMS IDK LSDVVMK AT EPQMVLFN I YDDWLDRIS SYTAFSRLTL LLRALKTNE E SAKMILLS DP TITIKSY HLW PSFTDE QWIT IESQM RDLIL TEYG RKYNVN ISA LTQTEIK DI ILGQNIKA P SVKRQKMAE LEAARSEKQN DEEAAGAST V MKTKTINA QG EEIVVVA SAD YESQTF SSKN EWRKS AIANT LLYL RLKNIY VSA DDFVEEQ NV YVLPKNLL K KFIEISDVK IQVAAFIYGM SAKDHPKVK E IKTVVLVP QL GHVGSVQ ISN IPDIGD LPDT EGLEL LGWIH TQTE ELKFMA ASE VATHSKL FA DKKRDCID I SIFSTPGSV SLSAYNLTDE GYQWGEENK D IMNVLSEG FE PTFSTHA QLL LSDRIT GNFI IPSGN VWNYT FMGT AFNQEG DYN FKYGIPL EF YNEMHRPV H FLQFSELAG DEELEAEQID VFS

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Macromolecule #4: Prp4

MacromoleculeName: Prp4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.953031 KDa
SequenceString: MSKYIALENL PVDLQHKGA T QNESTADI LK QLPHERL QAV LEKIPE EDLE VRRLL SILKK PEVV ENEDVQ QRR IRLAEIL MV DEIDLENI N NMENINGEE VDEEDDEDFF TPATSELIF A RRFLINYS LE RSRKRLQ KEM ERHQKF NTRQ ELLSR ...String:
MSKYIALENL PVDLQHKGA T QNESTADI LK QLPHERL QAV LEKIPE EDLE VRRLL SILKK PEVV ENEDVQ QRR IRLAEIL MV DEIDLENI N NMENINGEE VDEEDDEDFF TPATSELIF A RRFLINYS LE RSRKRLQ KEM ERHQKF NTRQ ELLSR RTELQ RMAN LELAGS QLV STKPISA VS LSTDDMVV A TGSWAGDLQ VLNSQTLQPL TQKLDSHVG K IGAIDWHP DS NNQMISC AED GLIKNF QYSN EEGGL RLLGD LVGH ERRISD VKY HPSGKFI GS ASHDMTWR L WDASTHQEL LLQEGHDKGV FSLSFQCDG S LVCSGGMD SL SMLWDIR SGS KVMTLA GHSK PIYTV AWSPN GYQV ATGGGD GII NVWDIRK RD EGQLNQIL A HRNIVTQVR FSKEDGGKKL VSCGYDNLI N VYSSDTWL KM GSLAGHT DKI ISLDIS NNSH FLVSG GWDRS IKLW N

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Macromolecule #5: Prp6

MacromoleculeName: Prp6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.644094 KDa
SequenceString: MERPSFLDQE PPAGYVPGI G RGATGFST KE KQVVSND DKG RRIPKR YREN LNNHL QSQPK DDED DEAANV FKT LELKLAQ KK KKRANEKD D DNSVDSSNV KRQFADLKES LAAVTESEW M DIPDATDF TR RNKRNRI QEQ LNRKTY AAPD SLIPG ...String:
MERPSFLDQE PPAGYVPGI G RGATGFST KE KQVVSND DKG RRIPKR YREN LNNHL QSQPK DDED DEAANV FKT LELKLAQ KK KKRANEKD D DNSVDSSNV KRQFADLKES LAAVTESEW M DIPDATDF TR RNKRNRI QEQ LNRKTY AAPD SLIPG NVDLN KLTE EREKLL QSQ IDENLAQ LT KNASNPIQ V NKPNAATDA LSYLKDLEND RVNSLSDAT L EDLQKMRT IL KSYRKAD PTN PQGWIA SARL EEKAR KFSVA KKII ENGCQE CPR SSDIWLE NI RLHESDVH Y CKTLVATAI NFNPTSPLLW FKAIDLEST T VNKYRVVR KA LQEIPRD EGL WKLAVS FEAD KAQVI KMLEK ATQF IPQSMD LLT AYTNLQS YH NAKMTLNS F RKILPQEPE IWIISTLLEE RNNPDIPVD K LVSLLKEG LL ELSKNGY KAT LSAWLK RAEA LNDAP NSNLT CQAI VYAILE WLR ESGEYES EL NNVDQILE K MPHSKVQIA VLKKLIQWDP CDTVLWSRL K MATESYHK IE ELLAFFQ ELL FQTKNS DDIR ANMRE KSPGL LMMY VSEYWK AQK GDTRQTL VL IDQIIDFA P HNLDLRFFK IKLLGRSLQL DELRDFFQQ T FSSLEDFK IS GTERLYY KYV NFLRYQ DLNE EAIKF LNERC LKSF PICHKF FLQ LGQIYHS MG NIEMSRET Y LSGTRLVPN CPLLWVSLSK IDEIDLKNP V RARSILDR GL LKNPDDV LFY IAKIQM EIRL GNLDQ AELLV TQAL QKFPSN ALL WVEQIKL FK HGNKSSLK K TIFQDALRR TQNDHRVLLE IGVSFYAEA Q YETSLKWL ER ALKKCSR YGD TWVWLF RTYA RLGKD TVDLY NMFD QCEPTY GPE WIAASKN VK MQYCTPRE I LLRLMNDK

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Macromolecule #6: Dib1

MacromoleculeName: Dib1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.480982 KDa
SequenceString:
MASVLLPQLR TGWHVDQAI V TETKRLVV IR FGRKNDR QCM IMDELL SSIA ERVRN FAVIY LCDI DEVSDF DEM YELTDPM TV MFFYHNKH M MCDFGTGNN NKLNFIVDDK QEMIDILET I FRGARKNK GL VVSPYDY NHK RVS

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Macromolecule #7: Prp31

MacromoleculeName: Prp31 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.128652 KDa
SequenceString: MSSEEDYFDE LEYDLADEV N EEKEDIQT KK LTTVNCQ TEK FNPFEI LPES IELFR TLALI SPDR LSLSET AQI LPKIVDL KR ILQQQEID F IKLLPFFNE IIPLIKSNIK LMHNFLISL Y SRRFPELS SL IPSPLQY SKV ISILEN ENYS KNESD ...String:
MSSEEDYFDE LEYDLADEV N EEKEDIQT KK LTTVNCQ TEK FNPFEI LPES IELFR TLALI SPDR LSLSET AQI LPKIVDL KR ILQQQEID F IKLLPFFNE IIPLIKSNIK LMHNFLISL Y SRRFPELS SL IPSPLQY SKV ISILEN ENYS KNESD ELFFH LENK AKLTRE QIL VLTMSMK TS FKNKEPLD I KTRTQILEA NSILENLWKL QEDIGQYIA S KISIIAPN VC FLVGPEI AAQ LIAHAG GVLE FSRIP SCNIA SIGK NKHLSH ELH TLESGVR QE GYLFASDM I QKFPVSVHK QMLRMLCAKV SLAARVDAG Q KNGDRNTV LA HKWKAEL SKK ARKLSE APSI SETKA LPIPE DQPK KKRAGR KFR KYKEKFR LS HVRQLQNR M EFGKQEQTV LDSYGEEVGL GMSNTSLQQ A VGATSGSR RS AGNQAKL TKV MKHRIS EANQ QADEF LISLG HNTE QPNLSP EMV QMHKKQH TN PEEETNWF S GHG

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Macromolecule #8: Prp3

MacromoleculeName: Prp3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.87025 KDa
SequenceString: MPPRNTYEK G NPKRQNSP YY KPSFLRR EET TNDEEK FQGH GLKTE LHSAL KSSN LNLIRR TYQ TGENPYL SD PHDRGSSS R FNRRYERGL KFYQKGEISK RIAQERTLQ K QQEEEELK RK LKQEEDE KDK RKLIES GDLP NLELH EDKFL LDLS ...String:
MPPRNTYEK G NPKRQNSP YY KPSFLRR EET TNDEEK FQGH GLKTE LHSAL KSSN LNLIRR TYQ TGENPYL SD PHDRGSSS R FNRRYERGL KFYQKGEISK RIAQERTLQ K QQEEEELK RK LKQEEDE KDK RKLIES GDLP NLELH EDKFL LDLS KFKIYY DNN HGYEWWD TA YLDEKGEL M EKYDMNGTS PAEEKLAEDI DEVDDDDDD E HPSIRYVA HP LPEKINE AKV SIKAYL TQHE RKRLR RNRRK MARE AREIKI KLG LLPKPEP KV KLSNMMSV F ENDQNITDP TAWEKVVKDQ VDLRKRKHL E ENERRHED AI KRRKEAV NMN VEKPTV YHCK VFQFK NLQNP KIRF KLKMNS KEL SLKGLCL RI RDDGPGII I VVGNEKSCK FYENLVMKRI KWNEDFELH T NTGDIKMD MH NNSISKT WEG YLQDCK FKGW FMKVC NDQDS LLRT LGQFDS EHF YSPVQT

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Macromolecule #9: Brr2

MacromoleculeName: Brr2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 202.6655 KDa
SequenceString: MTEHETKDKA KKIREIYRY D EMSNKVLK VD KRFMNTS QNP QRDAEI SQPK SMSGR ISAKD MGQG LCNNIN KGL KENDVAV EK TGKSASLK K IQQHNTILN SSSDFRLHYY PKDPSNVET Y EQILQWVT EV LGNDIPH DLI IGTADI FIRQ LKENE ...String:
MTEHETKDKA KKIREIYRY D EMSNKVLK VD KRFMNTS QNP QRDAEI SQPK SMSGR ISAKD MGQG LCNNIN KGL KENDVAV EK TGKSASLK K IQQHNTILN SSSDFRLHYY PKDPSNVET Y EQILQWVT EV LGNDIPH DLI IGTADI FIRQ LKENE ENEDG NIEE RKEKIQ HEL GINIDSL KF NELVKLMK N ITDYETHPD NSNKQAVAIL ADDEKSDEE E VTEMSNNA NV LGGEIND NED DDEEYD YNDV EVNSK KKNKR ALPN IENDII KLS DSKTSNI ES VPIYSIDE F FLQRKLRSE LGYKDTSVIQ DLSEKILND I ETLEHNPV AL EQKLVDL LKF ENISLA EFIL KNRST IFWGI RLAK STENEI PNL IEKMVAK GL NDLVEQYK F RETTHSKRE LDSGDDQPQS SEAKRTKFS N PAIPPVID LE KIKFDES SKL MTVTKV SLPE GSFKR VKPQY DEIH IPAPSK PVI DYELKEI TS LPDWCQEA F PSSETTSLN PIQSKVFHAA FEGDSNMLI C APTGSGKT NI ALLTVLK ALS HHYNPK TKKL NLSAF KIVYI APLK ALVQEQ VRE FQRRLAF LG IKVAELTG D SRLSRKQID ETQVLVSTPE KWDITTRNS N NLAIVELV RL LIIDEIH LLH DDRGPV LESI VARTF WASKY GQEY PRIIGL SAT LPNYEDV GR FLRVPKEG L FYFDSSFRP CPLSQQFCGI KERNSLKKL K AMNDACYE KV LESINEG NQI IVFVHS RKET SRTAT WLKNK FAEE NITHKL TKN DAGSKQI LK TEAANVLD P SLRKLIESG IGTHHAGLTR SDRSLSEDL F ADGLLQVL VC TATLAWG VNL PAHTVI IKGT DVYSP EKGSW EQLS PQDVLQ MLG RAGRPRY DT FGEGIIIT D QSNVQYYLS VLNQQLPIES QFVSKLVDN L NAEVVAGN IK CRNDAVN WLA YTYLYV RMLA SPMLY KVPDI SSDG QLKKFR ESL VHSALCI LK EQELVLYD A ENDVIEATD LGNIASSFYI NHASMDVYN R ELDEHTTQ ID LFRIFSM SEE FKYVSV RYEE KRELK QLLEK APIP IREDID DPL AKVNVLL QS YFSQLKFE G FALNSDIVF IHQNAGRLLR AMFEICLKR G WGHPTRML LN LCKSATT KMW PTNCPL RQFK TCPVE VIKRL EAST VPWGDY LQL ETPAEVG RA IRSEKYGK Q VYDLLKRFP KMSVTCNAQP ITRSVMRFN I EIIADWIW DM NVHGSLE PFL LMLEDT DGDS ILYYD VLFIT PDIV GHEFTL SFT YELKQHN QN NLPPNFFL T LISENWWHS EFEIPVSFNG FKLPKKFPP P TPLLENIS IS TSELGND DFS EVFEFK TFNK IQSQV FESLY NSND SVFVGS GKG TGKTAMA EL ALLNHWRQ N KGRAVYINP SGEKIDFLLS DWNKRFSHL A GGKIINKL GN DPSLNLK LLA KSHVLL ATPV QFELL SRRWR QRKN IQSLEL MIY DDAHEIS QG VYGAVYET L ISRMIFIAT QLEKKIRFVC LSNCLANAR D FGEWAGMT KS NIYNFSP SER IEPLEI NIQS FKDVE HISFN FSML QMAFEA SAA AAGNRNS SS VFLPSRKD C MEVASAFMK FSKAIEWDML NVEEEQIVP Y IEKLTDGH LR APLKHGV GIL YKGMAS NDER IVKRL YEYGA VSVL LISKDC SAF ACKTDEV II LGTNLYDG A EHKYMPYTI NELLEMVGLA SGNDSMAGK V LILTSHNM KA YYKKFLI EPL PTESYL QYII HDTLN NEIAN SIIQ SKQDCV DWF TYSYFYR RI HVNPSYYG V RDTSPHGIS VFLSNLVETC LNDLVESSF I EIDDTEAE VT AEVNGGD DEA TEIIST LSNG LIASH YGVSF FTIQ SFVSSL SNT STLKNML YV LSTAVEFE S VPLRKGDRA LLVKLSKRLP LRFPEHTSS G SVSFKVFL LL QAYFSRL ELP VDFQND LKDI LEKVV PLINV VVDI LSANGY LNA TTAMDLA QM LIQGVWDV D NPLRQIPHF NNKILEKCKE INVETVYDI M ALEDEERD EI LTLTDSQ LAQ VAAFVN NYPN VELTY SLNNS DSLI SGVKQK ITI QLTRDVE PE NLQVTSEK Y PFDKLESWW LVLGEVSKKE LYAIKKVTL N KETQQYEL EF DTPTSGK HNL TIWCVC DSYL DADKE LSFEI NVK

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Macromolecule #10: unknown proteins

MacromoleculeName: unknown proteins / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.528504 KDa
SequenceString:
XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX

+
Macromolecule #11: SmB

MacromoleculeName: SmB / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.183853 KDa
SequenceString: MSKIQVAHSS RLANLIDYK L RVLTQDGR VY IGQLMAF DKH MNLVLN ECIE ERVPK TQLDK LRPR KDSKDG TTL NIKVEKR VL GLTILRGE Q ILSTVVEDK PLLSKKERLV RDKKEKKQA Q KQTKLRKE KE KKPGKIA KPN TANAKH TSSN SREIA ...String:
MSKIQVAHSS RLANLIDYK L RVLTQDGR VY IGQLMAF DKH MNLVLN ECIE ERVPK TQLDK LRPR KDSKDG TTL NIKVEKR VL GLTILRGE Q ILSTVVEDK PLLSKKERLV RDKKEKKQA Q KQTKLRKE KE KKPGKIA KPN TANAKH TSSN SREIA QPSSS RYNG GNDNIG ANR SRFNNEA PP QTRKFQPP P GFKRK

+
Macromolecule #12: U4 SmD1

MacromoleculeName: U4 SmD1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.327998 KDa
SequenceString:
MKLVNFLKKL RNEQVTIEL K NGTTVWGT LQ SVSPQMN AIL TDVKLT LPQP RLNKL NSNGI AMAS LYLTGG QQP TASDNIA SL QYINIRGN T IRQIILPDS LNLDSLLVDQ KQLNSLRRS G QIANDPSK KR RRDFGAP ANK RPRRGL

+
Macromolecule #13: SmD2

MacromoleculeName: SmD2 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.021953 KDa
SequenceString:
MSSQIIDRPK HELSRAELE E LEEFEFKH GP MSLINDA MVT RTPVII SLRN NHKII ARVKA FDRH CNMVLE NVK ELWTEKK GK NVINRERF I SKLFLRGDS VIVVLKTPVE

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Macromolecule #14: SmD3

MacromoleculeName: SmD3 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.011384 KDa
SequenceString:
MTMNGIPVKL LNEAQGHIV S LELTTGAT YR GKLVESE DSM NVQLRD VIAT EPQGA VTHMD QIFV RGSQIK FIV VPDLLKN AP LFKKNSSR P MPPIRGPKR R

+
Macromolecule #15: SmE

MacromoleculeName: SmE / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.320758 KDa
SequenceString:
MSNKVKTKAM VPPINCIFN F LQQQTPVT IW LFEQIGI RIK GKIVGF DEFM NVVID EAVEI PVNS ADGKED VEK GTPLGKI LL KGDNITLI T SAD

+
Macromolecule #16: SmF

MacromoleculeName: SmF / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.178299 KDa
SequenceString:
MSESSDISAM QPVNPKPFL K GLVNHRVG VK LKFNSTE YRG TLVSTD NYFN LQLNE AEEFV AGVS HGTLGE IFI RCNNVLY IR ELPN

+
Macromolecule #17: SmG

MacromoleculeName: SmG / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.662906 KDa
SequenceString:
MVSTPELKKY MDKKILLNI N GSRKVAGI LR GYDIFLN VVL DDAMEI NGED PANNH QLGLQ TVIR GNSIIS LEA LDAI

+
Macromolecule #18: Snu66

MacromoleculeName: Snu66 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.367936 KDa
SequenceString: AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA ...String:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAR AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAATTK EAYKKLSQKF HGTKSNKK

+
Macromolecule #19: U5 SmE

MacromoleculeName: U5 SmE / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.362859 KDa
SequenceString:
MSNKVKTKAM VPPINCIFN F LQQQTPVT IW LFEQIGI RIK GKIVGF DEFM NVVID EAVEI PVNS ADGKED VEK GTPLGKI LL KGDNITLI T SAD

+
Macromolecule #20: U5 SmD1

MacromoleculeName: U5 SmD1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.200678 KDa
SequenceString:
MKLVNFLKKL RNEQVTIEL K NGTTVWGT LQ SVSPQMN AIL TDVKLT LPQP RLNKL NSNGI AMAS LYLTGG QQP TASDNIA SL QYINIRGN T IRQIILPDS LNLDSLLVDQ KQLNSLRRS G QIANDPSK KR RRDFGAP ANK RPRRGL

+
Macromolecule #22: Snu13

MacromoleculeName: Snu13 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.364584 KDa
SequenceString:
MSAPNPKAFP LADAALTQQ I LDVVQQAA NL RQLKKGA NEA TKTLNR GISE FIIMA ADCEP IEIL LHLPLL CED KNVPYVF VP SRVALGRA C GVSRPVIAA SITTNDASAI KTQIYAVKD K IETLLI

+
Macromolecule #23: LSm2

MacromoleculeName: LSm2 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.530101 KDa
SequenceString:
MLFFSFFKTL VDQEVVVEL K NDIEIKGT LQ SVDQFLN LKL DNISCT DEKK YPHLG SVRNI FIRG STVRYV YLN KNMVDTN LL QDATRREV M TERK

+
Macromolecule #24: LSm3

MacromoleculeName: LSm3 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.747967 KDa
SequenceString:
METPLDLLKL NLDERVYIK L RGARTLVG TL QAFDSHC NIV LSDAVE TIYQ LNNEE LSESE RRCE MVFIRG DTV TLISTPS ED DDGAVEI

+
Macromolecule #25: LSm4

MacromoleculeName: LSm4 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.594071 KDa
SequenceString: MLPLYLLTNA KGQQMQIEL K NGEIIQGI LT NVDNWMN LTL SNVTEY SEES AINSE DNAES SKAV KLNEIY IRG TFIKFIK LQ DNIIDKVK Q QINSNNNSN SNGPGHKRYY NNRDSNNNR G NYNRRNNN NG NSNRRPY SQN RQYNNS NSSN INNSI ...String:
MLPLYLLTNA KGQQMQIEL K NGEIIQGI LT NVDNWMN LTL SNVTEY SEES AINSE DNAES SKAV KLNEIY IRG TFIKFIK LQ DNIIDKVK Q QINSNNNSN SNGPGHKRYY NNRDSNNNR G NYNRRNNN NG NSNRRPY SQN RQYNNS NSSN INNSI NSINS NNQN MNNGLG GSV QHHFNSS SP QKVEF

+
Macromolecule #26: LSm5

MacromoleculeName: LSm5 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.458736 KDa
SequenceString:
MSLPEILPLE VIDKTINQK V LIVLQSNR EF EGTLVGF DDF VNVILE DAVE WLIDP EDESR NEKV MQHHGR MLL SGNNIAI LV PGGKKTPT E AL

+
Macromolecule #27: LSm6

MacromoleculeName: LSm6 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.227233 KDa
SequenceString:
MSGKASTEGS VTTEFLSDI I GKTVNVKL AS GLLYSGR LES IDGFMN VALS SATEH YESNN NKLL NKFNSD VFL RGTQVMY IS EQKI

+
Macromolecule #28: LSm7

MacromoleculeName: LSm7 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.233692 KDa
SequenceString:
MHQQHSKSEN KPQQQRKKF E GPKREAIL DL AKYKDSK IRV KLMGGK LVIG VLKGY DQLMN LVLD DTVEYM SNP DDENNTE LI SKNARKLG L TVIRGTILV SLSSAEGSDV LYMQK

+
Macromolecule #29: LSm8

MacromoleculeName: LSm8 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.1935 KDa
SequenceString:
MSATLKDYLN KRVVIIKVD G ECLIASLN GF DKNTNLF ITN VFNRIS KEFI CKAQL LRGSE IALV GLIDAE NDD SLAPIDE KK VPMLKDTK N KIENEHVIW EKVYESKTK

+
Macromolecule #30: Snu114

MacromoleculeName: Snu114 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 97.172828 KDa
SequenceString: MEGDDLFDEF GNLIGVDPF D SDEEESVL DE QEQYQTN TFE GSGNNN EIES RQLTS LGSKK ELGI SLEHPY GKE VEVLMET KN TQSPQTPL V EPVTERTKL QEHTIFTQLK KNIPKTRYN R DYMLSMAN IP ERIINVG VIG PLHSGK TSLM DLLVI ...String:
MEGDDLFDEF GNLIGVDPF D SDEEESVL DE QEQYQTN TFE GSGNNN EIES RQLTS LGSKK ELGI SLEHPY GKE VEVLMET KN TQSPQTPL V EPVTERTKL QEHTIFTQLK KNIPKTRYN R DYMLSMAN IP ERIINVG VIG PLHSGK TSLM DLLVI DSHKR IPDM SKNVEL GWK PLRYLDN LK QEIDRGLS I KLNGSTLLC TDLESKSRMI NFLDAPGHV N FMDETAVA LA ASDLVLI VID VVEGVT FVVE QLIKQ SIKNN VAMC FVINKL DRL ILDLKLP PM DAYLKLNH I IANINSFTK GNVFSPIDNN IIFASTKLG F TFTIKEFV SY YYAHSIP SSK IDDFTT RLWG SVYYH KGNFR TKPF ENVEKY PTF VEFILIP LY KIFSYALS M EKDKLKNLL RSNFRVNLSQ EALQYDPQP F LKHVLQLI FR QQTGLVD AIT RCYQPF ELFD NKTAH LSIPG KSTP EGTLWA HVL KTVDYGG AE WSLVRIYS G LLKRGDTVR ILDTSQSESR QKRQLHDIS K TETSNEDE DE DDETPSC EVE EIGLLG GRYV YPVHE AHKGQ IVLI KGISSA YIK SATLYSV KS KEDMKQLK F FKPLDYITE AVFKIVLQPL LPRELPKLL D ALNKISKY YP GVIIKVE ESG EHVILG NGEL YMDCL LYDLR ASYA KIEIKI SDP LTVFSES CS NESFASIP V SNSISRLGE ENLPGLSISV AAEPMDSKM I QDLSRNTL GK GQNCLDI DGI MDNPRK LSKI LRTEY GWDSL ASRN VWSFYN GNV LINDTLP DE ISPELLSK Y KEQIIQGFY WAVKEGPLAE EPIYGVQYK L LSISVPSD VN IDVMKSQ IIP LMKKAC YVGL LTAIP ILLEP IYEV DITVHA PLL PIVEELM KK RRGSRIYK T IKVAGTPLL EVRGQVPVIE SAGFETDLR L STNGLGMC QL YFWHKIW RKV PGDVLD KDAF IPKLK PAPIN SLSR DFVMKT RRR KGISTGG FM SNDGPTLE K YISAELYAQ LRENGLVP

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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

Concentration0.2 mg/mL
BufferpH: 7.9 / Component - Concentration: 1.0 mM / Component - Name: DTT
GridModel: Quantifoil R 1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 6.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Average exposure time: 16.0 sec. / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 473827
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

2966

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 23760
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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