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- EMDB-13793: Human 17S U2 snRNP 5' domain core -

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Basic information

Entry
Database: EMDB / ID: EMD-13793
TitleHuman 17S U2 snRNP 5' domain core
Map data
Sample
  • Complex: 17S U2 snRNP
    • Complex: 17S U2 snRNP
      • Protein or peptide: x 7 types
      • RNA: x 1 types
    • Complex: HIV Tat-specific factor 1
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordssnRNP / Spliceosome / U2 snRNP / Splicing / NUCLEAR PROTEIN
Function / homology
Function and homology information


U11/U12 snRNP / poly-ADP-D-ribose modification-dependent protein binding / B-WICH complex / chromatin-protein adaptor activity / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome ...U11/U12 snRNP / poly-ADP-D-ribose modification-dependent protein binding / B-WICH complex / chromatin-protein adaptor activity / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / 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 / 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 / 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: 2.21 Å
AuthorsTholen J / Galej WP
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)950278European Union
CitationJournal: Science / Year: 2022
Title: Structural basis of branch site recognition by the human spliceosome.
Authors: Jonas Tholen / Michal Razew / Felix Weis / Wojciech P Galej /
Abstract: Recognition of the intron branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is a critical event during spliceosome assembly. In mammals, BS sequences are poorly conserved, and ...Recognition of the intron branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is a critical event during spliceosome assembly. In mammals, BS sequences are poorly conserved, and unambiguous intron recognition cannot be achieved solely through a base-pairing mechanism. We isolated human 17 U2 snRNP and reconstituted in vitro its adenosine 5´-triphosphate (ATP)–dependent remodeling and binding to the pre–messenger RNA substrate. We determined a series of high-resolution (2.0 to 2.2 angstrom) structures providing snapshots of the BS selection process. The substrate-bound U2 snRNP shows that SF3B6 stabilizes the BS:U2 snRNA duplex, which could aid binding of introns with poor sequence complementarity. ATP-dependent remodeling uncoupled from substrate binding captures U2 snRNA in a conformation that competes with BS recognition, providing a selection mechanism based on branch helix stability.
History
DepositionOct 28, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13793.png

Downloads & links

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Map

FileDownload / File: emd_13793.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 640 pix.
= 409.6 Å		0.64 Å/pix.
x 640 pix.
= 409.6 Å		0.64 Å/pix.
x 640 pix.
= 409.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0062
Minimum - Maximum-0.016104283 - 0.04845517
Average (Standard dev.)-0.000012360203 (±0.00069275463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 409.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13793_msk_1.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Half map: #2

Fileemd_13793_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_13793_half_map_2.map
Projections & Slices
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Sample components

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Entire : 17S U2 snRNP

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

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Supramolecule #1: 17S U2 snRNP

SupramoleculeName: 17S U2 snRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: 17S U2 snRNP isolated from nuclear extract of HEK293F cells by affinity chromatography.
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: 17S U2 snRNP

SupramoleculeName: 17S U2 snRNP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6, #8-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HIV Tat-specific factor 1

SupramoleculeName: HIV Tat-specific factor 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Splicing factor 3B subunit 2

MacromoleculeName: Splicing factor 3B subunit 2 / type: protein_or_peptide / ID: 1 / 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 #2: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 2 / 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 #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: PHD finger-like domain-containing protein 5A

MacromoleculeName: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 4 / 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 #6: Splicing factor 3A subunit 3

MacromoleculeName: Splicing factor 3A subunit 3 / type: protein_or_peptide / ID: 6 / 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 #7: HIV Tat-specific factor 1

MacromoleculeName: HIV Tat-specific factor 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.88832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSSGMDEK TTGWRGGHVV EGLAGELEQL RARLEHHPQG QREPGGGGSS GTNLDGNDEF DEQLRMQELY GDGKDGDTQT DAGGEPDSL GQQPTDTPYE WDLDKKAWFP KITEDFIATY QANYGFSNDG ASSSTANVED VHARTAEEPP QEKAPEPTDA R KKGEKRKA ...String:
GPGSSGMDEK TTGWRGGHVV EGLAGELEQL RARLEHHPQG QREPGGGGSS GTNLDGNDEF DEQLRMQELY GDGKDGDTQT DAGGEPDSL GQQPTDTPYE WDLDKKAWFP KITEDFIATY QANYGFSNDG ASSSTANVED VHARTAEEPP QEKAPEPTDA R KKGEKRKA ESGWFHVEED RNTNVYVSGL PPDITVDEFI QLMSKFGIIM RDPQTEEFKV KLYKDNQGNL KGDGLCCYLK RE SVELALK LLDEDEIRGY KLHVEVAKFQ LKGEYDASKK KKKCKDYKKK LSMQQKQLDW RPERRAGPSR MRHERVVIIK NMF HPMDFE DDPLVLNEIR EDLRVECSKF GQIRKLLLFD RHPDGVASVS FRDPEEADYC IQTLDGRWFG GRQITAQAWD GTTD YQVEE TSREREERLR GWEAFLNAPE ANRGLRRSDS VSASERAGPS RARHFSEHPS TSKMNAQETA TGMAFEEPID EKKFE KTED GGEFEEGASE NNAKESSPEK EAEEGCPEKE SEEGCPKRGF EGSCSQKESE EGNPVRGSEE DSPKKESKKK TLKNDC EEN GLAKESEDDL NKESEEEVGP TKESEEDDSE KESDEDCSEK QSEDGSEREF EENGLEKDLD EEGSEKELHE NVLDKEL EE NDSENSEFED DGSEKVLDEE GSEREFDEDS DEKEEEEDTY EKVFDDESDE KEDEEYADEK GLEAADKKAE EGDADEKL F EESDDKEDED ADGKEVEDAD EKLFEDDDSN EKLFDEEEDS SEKLFDDSDE RGTLGGFGSV EEGPLSTGSS FILSSDDDD DDI

UniProtKB: 17S U2 SnRNP complex component HTATSF1

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Macromolecule #8: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 8 / 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 #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 #5: U2 snRNA

MacromoleculeName: U2 snRNA / type: rna / ID: 5 / 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: NR_002716.3

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 180 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.3 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride

Details: Sample after desalting may have also contained up to 5% glycerol.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 15531 / Average exposure time: 1.0 sec. / Average electron dose: 53.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 1500165
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 225934
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) / Software - details: Ab-initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6en4

chain_id: A, residue_range: 491-1304, source_name: PDB, initial_model_type: experimental model

6y5q

chain_id: B, residue_range: 452-598, source_name: PDB, initial_model_type: experimental model

6en4

chain_id: C, residue_range: 1-1217, source_name: PDB, initial_model_type: experimental model

6en4

chain_id: E, residue_range: 12-81, source_name: PDB, initial_model_type: experimental model

6en4

chain_id: G, residue_range: 8-90, source_name: PDB, initial_model_type: experimental model

6y5q

chain_id: 9, residue_range: 392-493, source_name: PDB, initial_model_type: experimental model
RefinementSpace: RECIPROCAL
Output model

PDB-7q3l:
Human 17S U2 snRNP 5' domain

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