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- EMDB-10688: 5'domain of human 17S U2 snRNP -

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Basic information

Entry
Database: EMDB / ID: EMD-10688
Title5'domain of human 17S U2 snRNP
Map data5'domain of human 17S U2 snRNP
Sample
  • Complex: human 17S U2 snRNP
    • Protein or peptide: Splicing factor 3A subunit 3
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 2
    • Protein or peptide: Splicing factor 3B subunit 3
    • Protein or peptide: Splicing factor 3B subunit 1
    • RNA: U2 snRNA
    • Protein or peptide: HIV Tat-specific factor 1
    • Protein or peptide: Probable ATP-dependent RNA helicase DDX46
  • Ligand: ZINC ION
Keywords17S U2 snRNP / SPLICING
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / chromatin-protein adaptor activity / splicing factor binding / U12-type spliceosomal complex / poly-ADP-D-ribose modification-dependent protein binding / protein localization to site of double-strand break / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type spliceosomal complex ...U11/U12 snRNP / B-WICH complex / chromatin-protein adaptor activity / splicing factor binding / U12-type spliceosomal complex / poly-ADP-D-ribose modification-dependent protein binding / protein localization to site of double-strand break / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / regulation of RNA splicing / mRNA 3'-splice site recognition / U2 snRNA binding / regulation of DNA repair / Cajal body / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA splicing, via spliceosome / fibrillar center / nuclear matrix / mRNA processing / site of double-strand break / RNA helicase activity / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
TatSF1-like, RNA recognition motif 1 / TatSF1-like / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / : / Replication stress response SDE2 C-terminal / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / : / SF3a60/Prp9 C-terminal ...TatSF1-like, RNA recognition motif 1 / TatSF1-like / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / : / Replication stress response SDE2 C-terminal / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / : / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Splicing factor 3B, subunit 5 / : / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / 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. / : / PPP2R1A-like HEAT repeat / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / RSE1/DDB1/CPSF1 first beta-propeller / DEAD-box subfamily ATP-dependent helicases signature. / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / 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-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
17S U2 SnRNP complex component HTATSF1 / Splicing factor 3B subunit 1 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Splicing factor 3B subunit 3 / Probable ATP-dependent RNA helicase DDX46 / PHD finger-like domain-containing protein 5A / Splicing factor 3B subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhang Z / Will CL
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nature / Year: 2020
Title: Molecular architecture of the human 17S U2 snRNP.
Authors: Zhenwei Zhang / Cindy L Will / Karl Bertram / Olexandr Dybkov / Klaus Hartmuth / Dmitry E Agafonov / Romina Hofele / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark /
Abstract: The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing. Stable addition of ...The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing. Stable addition of U2 during early spliceosome formation requires the DEAD-box ATPase PRP5. Yeast U2 small nuclear RNA (snRNA) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-interacting stem-loop (BSL), but whether the human U2 snRNA folds in a similar manner is unknown. The U2 SF3B1 protein, a common mutational target in haematopoietic cancers, contains a HEAT domain (SF3B1) with an open conformation in isolated SF3b, but a closed conformation in spliceosomes, which is required for stable interaction between U2 and the branch site. Here we report a 3D cryo-electron microscopy structure of the human 17S U2 snRNP at a core resolution of 4.1 Å and combine it with protein crosslinking data to determine the molecular architecture of this snRNP. Our structure reveals that SF3B1 interacts with PRP5 and TAT-SF1, and maintains its open conformation in U2 snRNP, and that U2 snRNA forms a BSL that is sandwiched between PRP5, TAT-SF1 and SF3B1. Thus, substantial remodelling of the BSL and displacement of BSL-interacting proteins must occur to allow formation of the U2-branch-site helix. Our studies provide a structural explanation of why TAT-SF1 must be displaced before the stable addition of U2 to the spliceosome, and identify RNP rearrangements facilitated by PRP5 that are required for stable interaction between U2 and the branch site.
History
DepositionFeb 24, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 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
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6y50
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10688.png

Downloads & links

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Map

FileDownload / File: emd_10688.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation5'domain of human 17S U2 snRNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.088184975 - 0.15606657
Average (Standard dev.)0.00045497718 (±0.0051613487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0880.1560.000

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Supplemental data

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Sample components

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Entire : human 17S U2 snRNP

EntireName: human 17S U2 snRNP
Components
  • Complex: human 17S U2 snRNP
    • Protein or peptide: Splicing factor 3A subunit 3
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 2
    • Protein or peptide: Splicing factor 3B subunit 3
    • Protein or peptide: Splicing factor 3B subunit 1
    • RNA: U2 snRNA
    • Protein or peptide: HIV Tat-specific factor 1
    • Protein or peptide: Probable ATP-dependent RNA helicase DDX46
  • Ligand: ZINC ION

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Supramolecule #1: human 17S U2 snRNP

SupramoleculeName: human 17S U2 snRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Splicing factor 3A subunit 3

MacromoleculeName: Splicing factor 3A subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.934844 KDa
SequenceString: METILEQQRR YHEEKERLMD VMAKEMLTKK STLRDQINSD HRTRAMQDRY MEVSGNLRDL YDDKDGLRKE ELNAISGPNE FAEFYNRLK QIKEFHRKHP NEICVPMSVE FEELLKAREN PSEEAQNLVE FTDEEGYGRY LDLHDCYLKY INLKASEKLD Y ITYLSIFD ...String:
METILEQQRR YHEEKERLMD VMAKEMLTKK STLRDQINSD HRTRAMQDRY MEVSGNLRDL YDDKDGLRKE ELNAISGPNE FAEFYNRLK QIKEFHRKHP NEICVPMSVE FEELLKAREN PSEEAQNLVE FTDEEGYGRY LDLHDCYLKY INLKASEKLD Y ITYLSIFD QLFDIPKERK NAEYKRYLEM LLEYLQDYTD RVKPLQDQNE LFGKIQAEFE KKWENGTFPG WPKETSSALT HA GAHLDLS AFSSWEELAS LGLDRLKSAL LALGLKCGGT LEERAQRLFS TKGKSLESLD TSLFAKNPKS KGTKRDTERN KDI AFLEAQ IYEYVEILGE QRHLTHENVQ RKQARTGEER EEEEEEQISE SESEDEENEI IYNPKNLPLG WDGKPIPYWL YKLH GLNIN YNCEICGNYT YRGPKAFQRH FAEWRHAHGM RCLGIPNTAH FANVTQIEDA VSLWAKLKLQ KASERWQPDT EEEYE DSSG NVVNKKTYED LKRQGLL

UniProtKB: Splicing factor 3A subunit 3

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Macromolecule #2: PHD finger-like domain-containing protein 5A

MacromoleculeName: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.427524 KDa
SequenceString:
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIV NLGSSKTDLF YERKKYGFKK R

UniProtKB: PHD finger-like domain-containing protein 5A

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Macromolecule #3: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.149369 KDa
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

UniProtKB: Splicing factor 3B subunit 5

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Macromolecule #4: Splicing factor 3B subunit 2

MacromoleculeName: Splicing factor 3B subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.377812 KDa
SequenceString: MATEHPEPPK AELQLPPPPP PGHYGAWAAQ ELQAKLAEIG APIQGNREEL VERLQSYTRQ TGIVLNRPVL RGEDGDKAAP PPMSAQLPG IPMPPPPLGL PPLQPPPPPP PPPPGLGLGF PMAHPPNLGP PPPLRVGEPV ALSEEERLKL AQQQAALLMQ Q EERAKQQG ...String:
MATEHPEPPK AELQLPPPPP PGHYGAWAAQ ELQAKLAEIG APIQGNREEL VERLQSYTRQ TGIVLNRPVL RGEDGDKAAP PPMSAQLPG IPMPPPPLGL PPLQPPPPPP PPPPGLGLGF PMAHPPNLGP PPPLRVGEPV ALSEEERLKL AQQQAALLMQ Q EERAKQQG DHSLKEHELL EQQKRAAVLL EQERQQEIAK MGTPVPRPPQ DMGQIGVRTP LGPRVAAPVG PVGPTPTVLP MG APVPRPR GPPPPPGDEN REMDDPSVGP KIPQALEKIL QLKESRQEEM NSQQEEEEME TDARSSLGQS ASETEEDTVS VSK KEKNRK RRNRKKKKKP QRVRGVSSES SGDREKDSTR SRGSDSPAAD VEIEYVTEEP EIYEPNFIFF KRIFEAFKLT DDVK KEKEK EPEKLDKLEN SAAPKKKGFE EEHKDSDDDS SDDEQEKKPE APKLSKKKLR RMNRFTVAEL KQLVARPDVV EMHDV TAQD PKLLVHLKAT RNSVPVPRHW CFKRKYLQGK RGIEKPPFEL PDFIKRTGIQ EMREALQEKE EQKTMKSKMR EKVRPK MGK IDIDYQKLHD AFFKWQTKPK LTIHGDLYYE GKEFETRLKE KKPGDLSDEL RISLGMPVGP NAHKVPPPWL IAMQRYG PP PSYPNLKIPG LNSPIPESCS FGYHAGGWGK PPVDETGKPL YGDVFGTNAA EFQTKTEEEE IDRTPWGELE PSDEESSE E EEEEESDEDK PDETGFITPA DSGLITPGGF SSVPAGMETP ELIELRKKKI EEAMDGSETP QLFTVLPEKR TATVGGAMM GSTHIYDMST VMSRKGPAPE LQGVEVALAP EELELDPMAM TQKYEEHVRE QQAQVEKEDF SDMVAEHAAK QKQKKRKAQP QDSRGGSKK YKEFKF

UniProtKB: Splicing factor 3B subunit 2

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Macromolecule #5: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.718844 KDa
SequenceString: MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVI LEYQPSKNMF EKIHQETFGK SGCRRIVPGQ FLAVDPKGRA VMISAIEKQK LVYILNRDAA ARLTISSPLE A HKANTLVY ...String:
MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVI LEYQPSKNMF EKIHQETFGK SGCRRIVPGQ FLAVDPKGRA VMISAIEKQK LVYILNRDAA ARLTISSPLE A HKANTLVY HVVGVDVGFE NPMFACLEMD YEEADNDPTG EAAANTQQTL TFYELDLGLN HVVRKYSEPL EEHGNFLITV PG GSDGPSG VLICSENYIT YKNFGDQPDI RCPIPRRRND LDDPERGMIF VCSATHKTKS MFFFLAQTEQ GDIFKITLET DED MVTEIR LKYFDTVPVA AAMCVLKTGF LFVASEFGNH YLYQIAHLGD DDEEPEFSSA MPLEEGDTFF FQPRPLKNLV LVDE LDSLS PILFCQIADL ANEDTPQLYV ACGRGPRSSL RVLRHGLEVS EMAVSELPGN PNAVWTVRRH IEDEFDAYII VSFVN ATLV LSIGETVEEV TDSGFLGTTP TLSCSLLGDD ALVQVYPDGI RHIRADKRVN EWKTPGKKTI VKCAVNQRQV VIALTG GEL VYFEMDPSGQ LNEYTERKEM SADVVCMSLA NVPPGEQRSR FLAVGLVDNT VRIISLDPSD CLQPLSMQAL PAQPESL CI VEMGGTEKQD ELGERGSIGF LYLNIGLQNG VLLRTVLDPV TGDLSDTRTR YLGSRPVKLF RVRMQGQEAV LAMSSRSW L SYSYQSRFHL TPLSYETLEF ASGFASEQCP EGIVAISTNT LRILALEKLG AVFNQVAFPL QYTPRKFVIH PESNNLIII ETDHNAYTEA TKAQRKQQMA EEMVEAAGED ERELAAEMAA AFLNENLPES IFGAPKAGNG QWASVIRVMN PIQGNTLDLV QLEQNEAAF SVAVCRFSNT GEDWYVLVGV AKDLILNPRS VAGGFVYTYK LVNNGEKLEF LHKTPVEEVP AAIAPFQGRV L IGVGKLLR VYDLGKKKLL RKCENKHIAN YISGIQTIGH RVIVSDVQES FIWVRYKRNE NQLIIFADDT YPRWVTTASL LD YDTVAGA DKFGNICVVR LPPNTNDEVD EDPTGNKALW DRGLLNGASQ KAEVIMNYHV GETVLSLQKT TLIPGGSESL VYT TLSGGI GILVPFTSHE DHDFFQHVEM HLRSEHPPLC GRDHLSFRSY YFPVKNVIDG DLCEQFNSME PNKQKNVSEE LDRT PPEVS KKLEDIRTRY AF

UniProtKB: Splicing factor 3B subunit 3

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Macromolecule #6: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146.024938 KDa
SequenceString: MAKIAKTHED IEAQIREIQG KKAALDEAQG VGLDSTGYYD QEIYGGSDSR FAGYVTSIAA TELEDDDDDY SSSTSLLGQK KPGYHAPVA LLNDIPQSTE QYDPFAEHRP PKIADREDEY KKHRRTMIIS PERLDPFADG GKTPDPKMNA RTYMDVMREQ H LTKEEREI ...String:
MAKIAKTHED IEAQIREIQG KKAALDEAQG VGLDSTGYYD QEIYGGSDSR FAGYVTSIAA TELEDDDDDY SSSTSLLGQK KPGYHAPVA LLNDIPQSTE QYDPFAEHRP PKIADREDEY KKHRRTMIIS PERLDPFADG GKTPDPKMNA RTYMDVMREQ H LTKEEREI RQQLAEKAKA GELKVVNGAA ASQPPSKRKR RWDQTADQTP GATPKKLSSW DQAETPGHTP SLRWDETPGR AK GSETPGA TPGSKIWDPT PSHTPAGAAT PGRGDTPGHA TPGHGGATSS ARKNRWDETP KTERDTPGHG SGWAETPRTD RGG DSIGET PTPGASKRKS RWDETPASQM GGSTPVLTPG KTPIGTPAMN MATPTPGHIM SMTPEQLQAW RWEREIDERN RPLS DEELD AMFPEGYKVL PPPAGYVPIR TPARKLTATP TPLGGMTGFH MQTEDRTMKS VNDQPSGNLP FLKPDDIQYF DKLLV DVDE STLSPEEQKE RKIMKLLLKI KNGTPPMRKA ALRQITDKAR EFGAGPLFNQ ILPLLMSPTL EDQERHLLVK VIDRIL YKL DDLVRPYVHK ILVVIEPLLI DEDYYARVEG REIISNLAKA AGLATMISTM RPDIDNMDEY VRNTTARAFA VVASALG IP SLLPFLKAVC KSKKSWQARH TGIKIVQQIA ILMGCAILPH LRSLVEIIEH GLVDEQQKVR TISALAIAAL AEAATPYG I ESFDSVLKPL WKGIRQHRGK GLAAFLKAIG YLIPLMDAEY ANYYTREVML ILIREFQSPD EEMKKIVLKV VKQCCGTDG VEANYIKTEI LPPFFKHFWQ HRMALDRRNY RQLVDTTVEL ANKVGAAEII SRIVDDLKDE AEQYRKMVME TIEKIMGNLG AADIDHKLE EQLIDGILYA FQEQTTEDSV MLNGFGTVVN ALGKRVKPYL PQICGTVLWR LNNKSAKVRQ QAADLISRTA V VMKTCQEE KLMGHLGVVL YEYLGEEYPE VLGSILGALK AIVNVIGMHK MTPPIKDLLP RLTPILKNRH EKVQENCIDL VG RIADRGA EYVSAREWMR ICFELLELLK AHKKAIRRAT VNTFGYIAKA IGPHDVLATL LNNLKVQERQ NRVCTTVAIA IVA ETCSPF TVLPALMNEY RVPELNVQNG VLKSLSFLFE YIGEMGKDYI YAVTPLLEDA LMDRDLVHRQ TASAVVQHMS LGVY GFGCE DSLNHLLNYV WPNVFETSPH VIQAVMGALE GLRVAIGPCR MLQYCLQGLF HPARKVRDVY WKIYNSIYIG SQDAL IAHY PRIYNDDKNT YIRYELDYIL

UniProtKB: Splicing factor 3B subunit 1

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Macromolecule #8: HIV Tat-specific factor 1

MacromoleculeName: HIV Tat-specific factor 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.965961 KDa
SequenceString: MSGTNLDGND EFDEQLRMQE LYGDGKDGDT QTDAGGEPDS LGQQPTDTPY EWDLDKKAWF PKITEDFIAT YQANYGFSND GASSSTANV EDVHARTAEE PPQEKAPEPT DARKKGEKRK AESGWFHVEE DRNTNVYVSG LPPDITVDEF IQLMSKFGII M RDPQTEEF ...String:
MSGTNLDGND EFDEQLRMQE LYGDGKDGDT QTDAGGEPDS LGQQPTDTPY EWDLDKKAWF PKITEDFIAT YQANYGFSND GASSSTANV EDVHARTAEE PPQEKAPEPT DARKKGEKRK AESGWFHVEE DRNTNVYVSG LPPDITVDEF IQLMSKFGII M RDPQTEEF KVKLYKDNQG NLKGDGLCCY LKRESVELAL KLLDEDEIRG YKLHVEVAKF QLKGEYDASK KKKKCKDYKK KL SMQQKQL DWRPERRAGP SRMRHERVVI IKNMFHPMDF EDDPLVLNEI REDLRVECSK FGQIRKLLLF DRHPDGVASV SFR DPEEAD YCIQTLDGRW FGGRQITAQA WDGTTDYQVE ETSREREERL RGWEAFLNAP EANRGLRRSD SVSASERAGP SRAR HFSEH PSTSKMNAQE TATGMAFEEP IDEKKFEKTE DGGEFEEGAS ENNAKESSPE KEAEEGCPEK ESEEGCPKRG FEGSC SQKE SEEGNPVRGS EEDSPKKESK KKTLKNDCEE NGLAKESEDD LNKESEEEVG PTKESEEDDS EKESDEDCSE KQSEDG SER EFEENGLEKD LDEEGSEKEL HENVLDKELE ENDSENSEFE DDGSEKVLDE EGSEREFDED SDEKEEEEDT YEKVFDD ES DEKEDEEYAD EKGLEAADKK AEEGDADEKL FEESDDKEDE DADGKEVEDA DEKLFEDDDS NEKLFDEEED SSEKLFDD S DERGTLGGFG SVEEGPLSTG SSFILSSDDD DDDI

UniProtKB: 17S U2 SnRNP complex component HTATSF1

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Macromolecule #9: Probable ATP-dependent RNA helicase DDX46

MacromoleculeName: Probable ATP-dependent RNA helicase DDX46 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.576484 KDa
SequenceString: MGRESRHYRK RSASRGRSGS RSRSRSPSDK RSKRGDDRRS RSRDRDRRRE RSRSRDKRRS RSRDRKRLRR SRSRERDRSR ERRRSRSRD RRRSRSRSRG RRSRSSSPGN KSKKTENRSR SKEKTDGGES SKEKKKDKDD KEDEKEKDAG NFDQNKLEEE M RKRKERVE ...String:
MGRESRHYRK RSASRGRSGS RSRSRSPSDK RSKRGDDRRS RSRDRDRRRE RSRSRDKRRS RSRDRKRLRR SRSRERDRSR ERRRSRSRD RRRSRSRSRG RRSRSSSPGN KSKKTENRSR SKEKTDGGES SKEKKKDKDD KEDEKEKDAG NFDQNKLEEE M RKRKERVE KWREEQRKKA MENIGELKKE IEEMKQGKKW SLEDDDDDED DPAEAEKEGN EMEGEELDPL DAYMEEVKEE VK KFNMRSV KGGGGNEKKS GPTVTKVVTV VTTKKAVVDS DKKKGELMEN DQDAMEYSSE EEEVDLQTAL TGYQTKQRKL LEP VDHGKI EYEPFRKNFY VEVPELAKMS QEEVNVFRLE MEGITVKGKG CPKPIKSWVQ CGISMKILNS LKKHGYEKPT PIQT QAIPA IMSGRDLIGI AKTGSGKTIA FLLPMFRHIM DQRSLEEGEG PIAVIMTPTR ELALQITKEC KKFSKTLGLR VVCVY GGTG ISEQIAELKR GAEIIVCTPG RMIDMLAANS GRVTNLRRVT YVVLDEADRM FDMGFEPQVM RIVDNVRPDR QTVMFS ATF PRAMEALARR ILSKPIEVQV GGRSVVCSDV EQQVIVIEEE KKFLKLLELL GHYQESGSVI IFVDKQEHAD GLLKDLM RA SYPCMSLHGG IDQYDRDSII NDFKNGTCKL LVATSVAARG LDVKHLILVV NYSCPNHYED YVHRAGRTGR AGNKGYAY T FITEDQARYA GDIIKALELS GTAVPPDLEK LWSDFKDQQK AEGKIIKKSS GFSGKGFKFD ETEQALANER KKLQKAALG LQDSDDEDAA VDIDEQIESM FNSKKRVKDM AAPGTSSVPA PTAGNAEKLE IAKRLALRIN AQKNLGIESQ DVMQQATNAI LRGGTILAP TVSAKTIAEQ LAEKINAKLN YVPLEKQEEE RQDGGQNESF KRYEEELEIN DFPQTARWKV TSKEALQRIS E YSEAAITI RGTYFPPGKE PKEGERKIYL AIESANELAV QKAKAEITRL IKEELIRLQN SYQPTNKGRY KVL

UniProtKB: Probable ATP-dependent RNA helicase DDX46

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Macromolecule #7: U2 snRNA

MacromoleculeName: U2 snRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.186445 KDa
SequenceString:
AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUGUAGUAUC UGUUCUUAUC AGUUUAAUAU CUGAUACGUC CUCUAUCCGA GGACAAUAU AUUAAAUGGA UUUUUGGAGC AGGGAGAUGG AAUAGGAGCU UGCUCCGUCC ACUCCACGCA UCGACCUGGU A UUGCAGUA CCUCCAGGAA CGGUGCACCC

GENBANK: GENBANK: X02665.1

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / 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 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: 1.0 sec. / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 120070
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6y50:
5'domain of human 17S U2 snRNP

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