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- EMDB-13028: The U2 part of Saccharomyces cerevisiae spliceosomal pre-A comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-13028
TitleThe U2 part of Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1)
Map data
Sample
  • Complex: S. cerevisiae spliceosomal pre-A complex
    • Protein or peptide: x 19 types
    • RNA: x 2 types
KeywordsS. cerevisiae / pre-A complex / Prp5 / U1 snRNP / U2 snRNP / prespliceosome / SPLICING
Function / homology
Function and homology information


mRNA branch site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / ATP-dependent activity, acting on RNA / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex ...mRNA branch site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / ATP-dependent activity, acting on RNA / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / RNA helicase / response to xenobiotic stimulus / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 ...Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / SF3B4, RNA recognition motif 1 / : / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / : / : / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Zinc-finger of C2H2 type / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / PPP2R1A-like HEAT repeat / Leucine-rich repeat / Small nuclear ribonucleoprotein Sm D3 / : / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / 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 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / : / Sm domain profile. / DEAD-box RNA helicase Q motif profile. / LSM domain superfamily / zinc finger / Zinc finger C2H2 superfamily / Leucine-rich repeat profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Zinc finger C2H2-type / Leucine-rich repeat / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Armadillo-like helical / helicase superfamily c-terminal domain / 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 / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RDS3 complex subunit 10 / Pre-mRNA-splicing factor PRP9 / Pre-mRNA-processing ATP-dependent RNA helicase PRP5 / Pre-mRNA-splicing factor PRP21 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / U2 small nuclear ribonucleoprotein B'' / Small nuclear ribonucleoprotein Sm D3 / U2 snRNP component HSH155 / Small nuclear ribonucleoprotein F ...RDS3 complex subunit 10 / Pre-mRNA-splicing factor PRP9 / Pre-mRNA-processing ATP-dependent RNA helicase PRP5 / Pre-mRNA-splicing factor PRP21 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / U2 small nuclear ribonucleoprotein B'' / Small nuclear ribonucleoprotein Sm D3 / U2 snRNP component HSH155 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Cold sensitive U2 snRNA suppressor 1 / Pre-mRNA-splicing factor RSE1 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor RDS3 / Pre-mRNA-splicing factor PRP11 / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein E / Protein HSH49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsZhang Z / Rigo N
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 860 Germany
CitationJournal: Nature / Year: 2021
Title: Structural insights into how Prp5 proofreads the pre-mRNA branch site.
Authors: Zhenwei Zhang / Norbert Rigo / Olexandr Dybkov / Jean-Baptiste Fourmann / Cindy L Will / Vinay Kumar / Henning Urlaub / Holger Stark / Reinhard Lührmann /
Abstract: During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly ...During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. ). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2-BS helix), which is proofread by Prp5 at this stage through an unclear mechanism. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2-BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155 to the bulged BS-A of the U2-BS helix triggers closure of Hsh155, which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155. Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing.
History
DepositionJun 3, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oqb
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13028.png

Downloads & links

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Map

FileDownload / File: emd_13028.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.32 Å/pix.
x 220 pix.
= 510.4 Å		2.32 Å/pix.
x 220 pix.
= 510.4 Å		2.32 Å/pix.
x 220 pix.
= 510.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.043786433 - 0.10472864
Average (Standard dev.)0.00027660112 (±0.0045616603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 510.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.322.322.32
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z510.400510.400510.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0440.1050.000

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Supplemental data

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Half map: #2

Fileemd_13028_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_13028_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : S. cerevisiae spliceosomal pre-A complex

EntireName: S. cerevisiae spliceosomal pre-A complex
Components
  • Complex: S. cerevisiae spliceosomal pre-A complex
    • Protein or peptide: U2 snRNP component HSH155
    • RNA: ACT1 pre-mRNA (delta-BS-A)
    • Protein or peptide: Pre-mRNA-splicing factor PRP11
    • Protein or peptide: Pre-mRNA-splicing factor PRP21
    • Protein or peptide: Pre-mRNA-splicing factor PRP9
    • Protein or peptide: Pre-mRNA-splicing factor RDS3
    • Protein or peptide: Cold sensitive U2 snRNA suppressor 1
    • Protein or peptide: Pre-mRNA-splicing factor RSE1
    • Protein or peptide: Protein HSH49
    • Protein or peptide: RDS3 complex subunit 10
    • Protein or peptide: U2 small nuclear ribonucleoprotein A'
    • Protein or peptide: U2 small nuclear ribonucleoprotein B''
    • 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: Pre-mRNA-processing ATP-dependent RNA helicase PRP5
    • RNA: U2 snRNA

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Supramolecule #1: S. cerevisiae spliceosomal pre-A complex

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

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Macromolecule #1: U2 snRNP component HSH155

MacromoleculeName: U2 snRNP component HSH155 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 110.166672 KDa
SequenceString: MSHPIQFVNA NNSDKSHQLG GQYSIPQDLR ENLQKEAARI GENEKDVLQE KMETRTVQNR EDSYHKRRFD MKFEPDSDTQ TVTSSENTQ DAVVPRKRKS RWDVKGYEPP DESSTAVKEN SDSALVNVEG IHDLMFFKPS DHKYFADVIS KKPIDELNKD E KKERTLSM ...String:
MSHPIQFVNA NNSDKSHQLG GQYSIPQDLR ENLQKEAARI GENEKDVLQE KMETRTVQNR EDSYHKRRFD MKFEPDSDTQ TVTSSENTQ DAVVPRKRKS RWDVKGYEPP DESSTAVKEN SDSALVNVEG IHDLMFFKPS DHKYFADVIS KKPIDELNKD E KKERTLSM LLLKIKNGNT ASRRTSMRIL TDKAVTFGPE MIFNRLLPIL LDRSLEDQER HLMIKTIDRV LYQLGDLTKP YV HKILVVA APLLIDEDPM VRSTGQEIIT NLSTVAGLKT ILTVMRPDIE NEDEYVRNVT SRAAAVVAKA LGVNQLLPFI NAA CHSRKS WKARHTGIKI VQQIGILLGI GVLNHLTGLM SCIKDCLMDD HVPVRIVTAH TLSTLAENSY PYGIEVFNVV LEPL WKGIR SHRGKVLSSF LKAVGSMIPL MDPEYAGYYT TEAMRIIRRE FDSPDDEMKK TILLVLQKCS AVESITPKFL REEIA PEFF QKFWVRRVAL DRPLNKVVTY TTVTLAKKLG CSYTIDKLLT PLRDEAEPFR TMAVHAVTRT VNLLGTADLD ERLETR LID ALLIAFQEQT NSDSIIFKGF GAVTVSLDIR MKPFLAPIVS TILNHLKHKT PLVRQHAADL CAILIPVIKN CHEFEML NK LNIILYESLG EVYPEVLGSI INAMYCITSV MDLDKLQPPI NQILPTLTPI LRNKHRKVEV NTIKFVGLIG KLAPTYAP P KEWMRICFEL LELLKSTNKE IRRSANATFG FIAEAIGPHD VLVALLNNLK VQERQLRVCT AVAIGIVAKV CGPYNVLPV IMNEYTTPET NVQNGVLKAM SFMFEYIGNM SKDYIYFITP LLEDALTDRD LVHRQTASNV ITHLALNCSG TGHEDAFIHL MNLLIPNIF ETSPHAIMRI LEGLEALSQA LGPGLFMNYI WAGLFHPAKN VRKAFWRVYN NMYVMYQDAM VPFYPVTPDN N EEYIEELD LVL

UniProtKB: U2 snRNP component HSH155

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Macromolecule #3: Pre-mRNA-splicing factor PRP11

MacromoleculeName: Pre-mRNA-splicing factor PRP11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.324467 KDa
SequenceString: MNYLEGVGSK KGGGGIASES QFNLQRRKEV ESLLSKGENV PYTFQDEKDD QVRSNPYIYK NHSGKLVCKL CNTMHMSWSS VERHLGGKK HGLNVLRRGI SIEKSSLGRE GQTTHDFRQQ QK(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...String:
MNYLEGVGSK KGGGGIASES QFNLQRRKEV ESLLSKGENV PYTFQDEKDD QVRSNPYIYK NHSGKLVCKL CNTMHMSWSS VERHLGGKK HGLNVLRRGI SIEKSSLGRE GQTTHDFRQQ QK(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)I IEAKQSLKNN GTIPVCKIAT VKNPKNGSVG LAIQ VNYSS EVKENSVDSD DKAKVPPLIR IVSGLELSDT KQKGKKFLVI AYEPFENIAI ELPPNEILFS ENNDMDNNND GVDEL NKKC TFWDAISKLY YVQFFFKQAE QEQADV

UniProtKB: Pre-mRNA-splicing factor PRP11

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Macromolecule #4: Pre-mRNA-splicing factor PRP21

MacromoleculeName: Pre-mRNA-splicing factor PRP21 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 33.111512 KDa
SequenceString: MEPEDTQLKE DIKTTVNYIK QHGVEFENKL LEDERFSFIK KDDPLHEYYT KLMNEPTDTV SGEDNDRKSE REIARPPDFL FSQYDTGIS RRDMEVIKLT ARYYAKDKSI VEQMISKDGE ARLNFMNSSH PLHKTFTDFV AQYKRVYSFT GQEIKKSKRT I LDNCFERT ...String:
MEPEDTQLKE DIKTTVNYIK QHGVEFENKL LEDERFSFIK KDDPLHEYYT KLMNEPTDTV SGEDNDRKSE REIARPPDFL FSQYDTGIS RRDMEVIKLT ARYYAKDKSI VEQMISKDGE ARLNFMNSSH PLHKTFTDFV AQYKRVYSFT GQEIKKSKRT I LDNCFERT QYWEFEKDKD REHDKLVELC KIQFAAIPWD KFTQVAKFSI PEDTEIFEGS LDLEQMRLRR VQTGIKLFDS IK PTNEEEK IVSDQGKQKG GDSKGKKRKI RAVGETRLKK SKK

UniProtKB: Pre-mRNA-splicing factor PRP21

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Macromolecule #5: Pre-mRNA-splicing factor PRP9

MacromoleculeName: Pre-mRNA-splicing factor PRP9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 63.126445 KDa
SequenceString: MNLLETRRSL LEEMEIIENA IAERIQRNPE LYYHYIQESS KVFPDTKLPR SSLIAENKIY KFKKVKRKRK QIILQQHEIN IFLRDYQEK QQTFNKINRP EETQEDDKDL PNFERKLQQL EKELKNEDEN FELDINSKKD KYALFSSSSD PSRRTNILSD R ARDLDLNE ...String:
MNLLETRRSL LEEMEIIENA IAERIQRNPE LYYHYIQESS KVFPDTKLPR SSLIAENKIY KFKKVKRKRK QIILQQHEIN IFLRDYQEK QQTFNKINRP EETQEDDKDL PNFERKLQQL EKELKNEDEN FELDINSKKD KYALFSSSSD PSRRTNILSD R ARDLDLNE IFTRDEQYGE YMELEQFHSL WLNVIKRGDC SLLQFLDILE LFLDDEKYLL TPPMDRKNDR YMAFLLKLSK YV ETFFFKS YALLDAAAVE NLIKSDFEHS YCRGSLRSEA KGIYCPFCSR WFKTSSVFES HLVGKIHKKN ESKRRNFVYS EYK LHRYLK YLNDEFSRTR SFVERKLAFT ANERMAEMDI LTQKYEAPAY DSTEKEGAEQ VDGEQRDGQL QEEHLSGKSF DMPL GPDGL PMPYWLYKLH GLDREYRCEI CSNKVYNGRR TFERHFNEER HIYHLRCLGI EPSSVFKGIT KIKEAQELWK NMQGQ SQLT SIAAVPPKPN PSQLKVPTEL ELEEEDEEGN VMSKKVYDEL KKQGLV

UniProtKB: Pre-mRNA-splicing factor PRP9

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Macromolecule #6: Pre-mRNA-splicing factor RDS3

MacromoleculeName: Pre-mRNA-splicing factor RDS3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.283573 KDa
SequenceString:
MSRHQFDLIM CLKQPGVQTG LLCEKCDGKC PICDSYVRPK RKVRVCENCS FGKQAKNCII CNLNVGVNDA FYCWECCRLG KDKDGCPRI LNLGSNRLDR HFEKKKKV

UniProtKB: Pre-mRNA-splicing factor RDS3

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Macromolecule #7: Cold sensitive U2 snRNA suppressor 1

MacromoleculeName: Cold sensitive U2 snRNA suppressor 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.339879 KDa
SequenceString: MARTKSRKRS GNNQNKNASV VNNKAEIAAM IDARRLEQKK KGGVTNSKGK TNKVVDAKLE KEFKDVLQRF QVQENDTPKE ITKDEKNNH VVIVEKNPVM NRKHTAEDEL EDTPSDGIEE HLSARKRRKT EKPSLSQLKS QVPYPQIIEW YDCDARYPGL L ASIKCTKN ...String:
MARTKSRKRS GNNQNKNASV VNNKAEIAAM IDARRLEQKK KGGVTNSKGK TNKVVDAKLE KEFKDVLQRF QVQENDTPKE ITKDEKNNH VVIVEKNPVM NRKHTAEDEL EDTPSDGIEE HLSARKRRKT EKPSLSQLKS QVPYPQIIEW YDCDARYPGL L ASIKCTKN VIPVPSHWQS KKEYLSGRSL LGKRPFELPD IIKKTNIEQM RSTLPQSGLD GQDEKSLKEA SRARVQPKMG AL DLDYKKL HDVFFKIGAN WKPDHLLCFG DVYYENRNLF EETNWKRMVD HKRPGRISQE LRAIMNLPEG QLPPWCMKMK DIG LPTGYP DLKIAGLNWD ITNLKGDVYG KIIPNHHSRS KKQGRNYFGA LISFETPEFE NSKEDTQANA ENGRQDDKID DEVE HKLDH FQEDISEVTS AEEKLERNEE ESEKQLYTVL K

UniProtKB: Cold sensitive U2 snRNA suppressor 1

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Macromolecule #8: Pre-mRNA-splicing factor RSE1

MacromoleculeName: Pre-mRNA-splicing factor RSE1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 153.956781 KDa
SequenceString: MWGGGKMAVV SLSPHTAKMR KLFGQASTTM AYDGLKREAE RRTRSDHNIT MVAKDDELYL YHLTLKKQTN FVHSCIGHFV DLEAGSKRE QSQLCVATET HLELYDTADG ELKLIAKFQN LFATITSMKS LDLPHSGSRA KASNWPTFLA LTSDSGNLSI V QIIMHAGA ...String:
MWGGGKMAVV SLSPHTAKMR KLFGQASTTM AYDGLKREAE RRTRSDHNIT MVAKDDELYL YHLTLKKQTN FVHSCIGHFV DLEAGSKRE QSQLCVATET HLELYDTADG ELKLIAKFQN LFATITSMKS LDLPHSGSRA KASNWPTFLA LTSDSGNLSI V QIIMHAGA LRLKTLVNQP LTRTTLRRVS PISYMEIDPN GRCIILSSVE QNKLCFLVDY AQKLRISSPL EIIRPHMVTL DM AVVDVNF NNPCFVTLEI DNAATQLSVH LIFYVLELGL NHIVKKADYL VNPSANFVLS LPDLSRYNIT TSLSDNNYDA DYD TLFNPF VVIGFENHIL VKDMNGFFSL KVEIPKRSIT NSRHKNVTII SGIVQKLKND FFVLLQSNHG DLFKLTVSPD TNDR NRPLV QLSYFDTIQN SHQLHIFKNG YLFALSEMNN NFLFQFEKLG VEKNDFSNVL TSKDPNKSLV FEPSIKLQNL SILSQ QLNL NPSIKSQIVS DSPLSIATKH FTNNKIITLT NAVNYSNLIS TSLPPNATKL WLIPDPATTG DNNTLLFITF PKKTMI LQI DNESMEELTP DEATRSAFKL SQDTTIHTCL MGSHSIIQVC TAELRHIVPT GKSRYSNKLT WVPPAGIRIV CATSSKT QL IISLSNYELV YFKIDVSSDS LIELTTHPEL DTMPSKVAIV QDTQHADLLA IADNEGMIKI MSLKDQKEDF LTVISLQL V SEKISDMIMV RDSSIGQLNL HVGLENGVYM KFHIGDVDGS FTDIKRRFLG LKPVSLSYLR EISVSLNNEE EEEEEEDDD DEKEEEEINS SGAKWMSCVV CHSSSTWVSY TWKNVWTIRQ LKDQNMLSCS KFVNADVAIN GVCSISSSGR LNIGRVSNFP TLDNWFHVH ESSVNKQENG GGDESNEEEE DEMEEEMEML QISTFRPRTI LSFPNNPKSI LFIDNHSGKK QCRISLQIDG E CLKFGSSD HLYKILDDID CVSAAIIDFT RQADHLIICA GDKRLLTYKI LVNKDKLSFD IELLHQTEII SPIHAMLKFK NF LLTAMGS TIVLYGLGKK QLLRRSVTQT PVSITKIVSM HQWNYERLAV GDIHESVTLF IWDPAGNVFI PYVDDSVKRH VTV LKFLDE ATVIGADRYG NAWTLRSPPE CEKIMSNHDP SELSNGAIKY PLDVITLQQK LPNTYDCKFK FQLLNHFFVN DIIT DFHIL DSLSNSDRPG CIYMGLQGTV GCFIPLLSKG NVFMMGNIEN IMAEADDTFY LDYESRKKNN NMRKEDDEEE SGSVV LQGR HGIEDEIICE GSCSILGRDH QEYRSYYAPV RKVIDGDLCE NFLRLSLNEQ EFLAKNLKSV QVEDIIQTIN EVRTNY M

UniProtKB: Pre-mRNA-splicing factor RSE1

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Macromolecule #9: Protein HSH49

MacromoleculeName: Protein HSH49 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.534152 KDa
SequenceString: MNYSADSGNT VYVGNIDPRI TKEQLYELFI QINPVLRIKY PKDKVLQAYQ GYAFIEFYNQ GDAQYAIKIM NNTVRLYDRL IKVRQVTNS TGTTNLPSNI SKDMILPIAK LFIKNLADSI DSDQLVKIFN KFGKLIREPE IFYLSNGKLK CAYVYFEDFE K ADLAIKSL ...String:
MNYSADSGNT VYVGNIDPRI TKEQLYELFI QINPVLRIKY PKDKVLQAYQ GYAFIEFYNQ GDAQYAIKIM NNTVRLYDRL IKVRQVTNS TGTTNLPSNI SKDMILPIAK LFIKNLADSI DSDQLVKIFN KFGKLIREPE IFYLSNGKLK CAYVYFEDFE K ADLAIKSL NNQLVANNRI TVDYAFKENG KGNAKYGDDV DRLLNKEALK HNMLK

UniProtKB: Protein HSH49

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Macromolecule #10: RDS3 complex subunit 10

MacromoleculeName: RDS3 complex subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.888207 KDa
SequenceString:
MAEKQRQLKL QKIYKQKYIG LGDESTTREQ WQRNVRNDTL NTLQGHSASL EYVSLSRGDL SIRDTRIHLL KSMSPGYKAY LREE

UniProtKB: RDS3 complex subunit 10

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Macromolecule #11: U2 small nuclear ribonucleoprotein A'

MacromoleculeName: U2 small nuclear ribonucleoprotein A' / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.232252 KDa
SequenceString: MKFTPSIVID APQYYVDHFN GKYNVDKCVI LRDLQLETDS ESMPSSLKHL TKPTHILDLT NNDLIMIPDL SRRDDIHTLL LGRNNIVEV DGRLLPMNVQ NLTLSNNSIR RFEDLQRLRR APRTLKNLTL IGNQVCHLAN YREHVLRLVP HLETLDFQNV T AEERKSAM ...String:
MKFTPSIVID APQYYVDHFN GKYNVDKCVI LRDLQLETDS ESMPSSLKHL TKPTHILDLT NNDLIMIPDL SRRDDIHTLL LGRNNIVEV DGRLLPMNVQ NLTLSNNSIR RFEDLQRLRR APRTLKNLTL IGNQVCHLAN YREHVLRLVP HLETLDFQNV T AEERKSAM SFPRQADGDT LGPVNTAIRD NGSRDKTMEI MNLVVSKMTV ERRNELKKQL AEATSLEEIA RLEKLLSGGV

UniProtKB: U2 small nuclear ribonucleoprotein A'

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Macromolecule #12: U2 small nuclear ribonucleoprotein B''

MacromoleculeName: U2 small nuclear ribonucleoprotein B'' / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.850944 KDa
SequenceString:
MVEPARKKQR IDRDTHHTVA EPVTEAKNTL YVSQLNEKIN MQRLRVNLFL LFATFGEVLK VSMNFKKQRG QAFITMRTID QASLAQISL NGERFFGKPL KVEFSKSETK TL

UniProtKB: U2 small nuclear ribonucleoprotein B''

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Macromolecule #13: Small nuclear ribonucleoprotein-associated protein B

MacromoleculeName: Small nuclear ribonucleoprotein-associated protein B / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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 #14: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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 #15: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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 #16: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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 #17: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.27001 KDa
SequenceString:
MSNKVKTKAM VPPINCIFNF LQQQTPVTIW LFEQIGIRIK GKIVGFDEFM NVVIDEAVEI PVNSADGKED VEKGTPLGKI LLKGDNITL ITSA

UniProtKB: Small nuclear ribonucleoprotein E

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Macromolecule #18: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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 #19: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.490809 KDa
SequenceString:
MVSTPELKKY MDKKILLNIN GSRKVAGILR GYDIFLNVVL DDAMEINGED PANNHQLGLQ TVIRGNSIIS LEALDAI

UniProtKB: Small nuclear ribonucleoprotein G

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Macromolecule #20: Pre-mRNA-processing ATP-dependent RNA helicase PRP5

MacromoleculeName: Pre-mRNA-processing ATP-dependent RNA helicase PRP5 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 96.512125 KDa
SequenceString: METIDSKQNI NRESLLEERR KKLAKWKQKK AQFDAQKEHQ TSRNDIVTNS LEGKQTTEKF TERQERVKEE LRKRKNEFRK SDEPVSVKP SKKKSKRSKV KKKISFDFSD DDDSEIGVSF RSKEHIQKAP EHDNEKDPLD EFMTSLKEEK MSNSKGMYDR G DILDVEDQ ...String:
METIDSKQNI NRESLLEERR KKLAKWKQKK AQFDAQKEHQ TSRNDIVTNS LEGKQTTEKF TERQERVKEE LRKRKNEFRK SDEPVSVKP SKKKSKRSKV KKKISFDFSD DDDSEIGVSF RSKEHIQKAP EHDNEKDPLD EFMTSLKEEK MSNSKGMYDR G DILDVEDQ LFELGGTDDE DVEDNTDNSN IAKIAKLKAK KRVKQIYYSP EELEPFQKNF YIESETVSSM SEMEVEELRL SL DNIKIKG TGCPKPVTKW SQLGLSTDTM VLITEKLHFG SLTPIQSQAL PAIMSGRDVI GISKTGSGKT ISYLLPLLRQ VKA QRPLSK HETGPMGLIL APTRELALQI HEEVTKFTEA DTSIRSVCCT GGSEMKKQIT DLKRGTEIVV ATPGRFIDIL TLND GKLLS TKRITFVVMD EADRLFDLGF EPQITQIMKT VRPDKQCVLF SATFPNKLRS FAVRVLHSPI SITINSKGMV NENVK QKFR ICHSEDEKFD NLVQLIHERS EFFDEVQSEN DGQSSDVEEV DAKAIIFVSS QNICDFISKK LLNAGIVTCA IHAGKP YQE RLMNLEKFKR EKNSILLCTE VLSRGLNVPE VSLVIIYNAV KTFAQYVHTT GRTARGSRSG TAITLLLHDE LSGAYIL SK AMRDEEIKAL DPLQAKELQE MSAKFESGMK KGKFRLSKGF GGKGLENIKS KREEAQNKDL ELKKNDKRSD DLEKKISN P REGHDSVSES SALIPRLNYE LFKESTDGSI IFYAKVYIND LPQIVRWEAT KNTTLLFIKH ETGCSITNKG KFYPEGKEP KNENDEPKLY LLIEGQDEKD IQLSIELLEQ KVKEGVVKAA SLSLKSTKY

UniProtKB: Pre-mRNA-processing ATP-dependent RNA helicase PRP5

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Macromolecule #2: ACT1 pre-mRNA (delta-BS-A)

MacromoleculeName: ACT1 pre-mRNA (delta-BS-A) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 101.208961 KDa
SequenceString: AUGGAUUCUG GUAUGUUCUA GCGCUUGCAC CAUCCCAUUU AACUGUAAGA AGAAUUGCAC GGUCCCAAUU GCUCGAGAGA UUUCUCUUU UACCUUUUUU UACUAUUUUU CACUCUCCCA UAACCUCCUA UAUUGACUGA UCUGUAAUAA CCACGAUAUU A UUGGAAUA ...String:
AUGGAUUCUG GUAUGUUCUA GCGCUUGCAC CAUCCCAUUU AACUGUAAGA AGAAUUGCAC GGUCCCAAUU GCUCGAGAGA UUUCUCUUU UACCUUUUUU UACUAUUUUU CACUCUCCCA UAACCUCCUA UAUUGACUGA UCUGUAAUAA CCACGAUAUU A UUGGAAUA AAUAGGGGCU UGAAAUUUGG AAAAAAAAAA AAAACUGAAA UAUUUUCGUG AUAAGUGAUA GUGAUAUUCU UC UUUUAUU UGCUACUGUU ACUAAGUCUC AUGUACUACA UCGAUUGCUU CAUUCUUUUU GUUGCUAUAU UAUAUGUUUA G

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Macromolecule #21: U2 snRNA

MacromoleculeName: U2 snRNA / type: rna / ID: 21 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 376.267406 KDa
SequenceString: ACGAAUCUCU UUGCCUUUUG GCUUAGAUCA AGUGUAGUAU CUGUUCUUUU CAGUGUAACA ACUGAAAUGA CCUCAAUGAG GCUCAUUAC CUUUUAAUUU GUUACAAUAC ACAUUUUUUG GCACCCAAAA UAAUAAAAUG GACGGGAAGA GACUUUUUAA G CAAGUUGU ...String:
ACGAAUCUCU UUGCCUUUUG GCUUAGAUCA AGUGUAGUAU CUGUUCUUUU CAGUGUAACA ACUGAAAUGA CCUCAAUGAG GCUCAUUAC CUUUUAAUUU GUUACAAUAC ACAUUUUUUG GCACCCAAAA UAAUAAAAUG GACGGGAAGA GACUUUUUAA G CAAGUUGU UUUCCGCUAA UGUCAGGUCU CACUACUUUU UGCUGCUAUU UUUCUUCGCU CAUGGUUUCU UCAUAAGGCG UU UUUAUGA UGGUUUUUCG AAAUUGGUUU UUGAGACGAC GGUUGCUCAA GGUUAUUGUU UUUGUUUUCU UCUGGUUGUU UUC UAUUUU CUUUUUUUUA GCUUUCUGUU UCUCCCUUAG UUUGGCUUUU UGCUUCAUAC UCUUCCCUGU CUUUCCGAGC CGUU UAUGU CCAACGCGGG AUUUGGUUUU UCUUUAUCGA UGGGAAGAAA UGGUGCUAUA GUAGGUUGGG AGAUAAUAUU UAUGG UAUG GGGUGCUAGU GCGGAUGGGG CGCUCUUAUU GUUGAUUUCU UCGCUCGUCU UCUUUUUCUG GUGGCGCUGC AAGAGG AAG UUUUUCGACU UUGUUAUGAU UUUUGGUUUG CAAGGAAAGG UGUCUUACGA UUCUUUUUUU GAUGUAAUAG GAUAAGC UU GCUUAUCCCC CAAGUAUCGG CCAAAGUUGU UGAUUUUCCU UUUGAAGUGU CCUCGGUUUG AGGGGGUGUA GGGUGGGG U UGGUCUACAA UAAGAGUGUU CCAUUGUUAA CGUGCUGGCG UCUUUUACUA UAUUUUUUUU CCCAGUUUAU UUUGUGCUU AUUUUCUCAU UGAGGAGAAG GAGCUCUUCU CGCAGGAUAU AAAUGGAGGU UUGCUAAAGG GGAGGAGAUG UGUUUGUGAG AAUACUGCU GAGAGAGUUC UGGAAGAGAA AAAAAGGAGG CAAUGGAAGG CGUUUGCUGG GAAAAGAGAA GAGCCAUGAC U GCAUCUGU UGUUUCAAGG CCAGUUUUAU UAACCGCCUA UGUCAUAGAG GCGUUUUUUU UGGAGGGAUU UGAAGAAUGC CG GCGGCAU CAAGAAACGG ACUUGAUGGU UGACGCCUGU UUUUAAAGUU AGAGACGUCG CGACCCUCGC ACUUGUGGAG UCG UUCUUG ACUUUUACUU UGGUCGCUUG AUGUUUCUCU CGUCUUCCCG UUCGCUCUU

GENBANK: GENBANK: Z36099.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.02 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 160894
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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