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- EMDB-13811: Substrate-bound A-like U2 snRNP -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-13811
TitleSubstrate-bound A-like U2 snRNP
Map data
Sample
  • Complex: A-like U2 snRNP
    • Complex: A-like U2 snRNP
      • Protein or peptide: x 8 types
      • RNA: x 1 types
    • Complex: BPS oligo
      • RNA: x 1 types
  • Ligand: x 2 types
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / : / 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 / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA 3'-splice site recognition / regulation of DNA repair / U2 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / positive regulation of neuron projection development / mRNA splicing, via spliceosome / mRNA processing / nuclear matrix / 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 / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
SF3B6, RNA recognition motif / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / : / Replication stress response SDE2 C-terminal / Cactus-binding C-terminus of cactin protein / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain ...SF3B6, RNA recognition motif / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / : / Replication stress response SDE2 C-terminal / Cactus-binding C-terminus of cactin protein / 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 / 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) / 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) / Matrin/U1-C, C2H2-type zinc finger / Splicing factor 3B subunit 1-like / Zinc finger matrin-type profile. / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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 / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Splicing factor 3B subunit 1 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Splicing factor 3B subunit 3 / Splicing factor 3A subunit 2 / PHD finger-like domain-containing protein 5A / Splicing factor 3B subunit 5 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 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
DepositionNov 1, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13811.png

Downloads & links

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Map

FileDownload / File: emd_13811.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00561
Minimum - Maximum-0.0149930045 - 0.052430067
Average (Standard dev.)-6.8634847e-07 (±0.0007333104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 409.60022 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13811_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map postprocessed in relion with -40 B-factor.

Fileemd_13811_additional_1.map
AnnotationMap postprocessed in relion with -40 B-factor.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13811_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13811_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A-like U2 snRNP

EntireName: A-like U2 snRNP
Components
  • Complex: A-like U2 snRNP
    • Complex: A-like U2 snRNP
      • Protein or peptide: Splicing factor 3A subunit 2
      • RNA: U2 snRNAU2 spliceosomal RNA
      • Protein or peptide: Splicing factor 3A subunit 3
      • Protein or peptide: Splicing factor 3B subunit 1
      • 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: Splicing factor 3B subunit 6
      • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Complex: BPS oligo
      • RNA: BPS oligo
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: A-like U2 snRNP

SupramoleculeName: A-like U2 snRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Details: Spliceosomal complex A-like U2 snRNP generated by binding BPS oligo to 17S U2 snRNP that was isolated from nuclear extract of HEK293F cells by affinity chromatography.
Molecular weightTheoretical: 1.08 MDa

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Supramolecule #2: A-like U2 snRNP

SupramoleculeName: A-like U2 snRNP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9 / Details: Spliceosomal complex A-like U2 snRNP
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BPS oligo

SupramoleculeName: BPS oligo / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #10 / Details: Spliceosomal complex A-like U2 snRNP
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: Splicing factor 3A subunit 2

MacromoleculeName: Splicing factor 3A subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 49.327355 KDa
SequenceString: MDFQHRPGGK TGSGGVASSS ESNRDRRERL RQLALETIDI NKDPYFMKNH LGSYECKLCL TLHNNEGSYL AHTQGKKHQT NLARRAAKE AKEAPAQPAP EKVKVEVKKF VKIGRPGYKV TKQRDSEMGQ QSLLFQIDYP EIAEGIMPRH RFMSAYEQRI E PPDRRWQY ...String:
MDFQHRPGGK TGSGGVASSS ESNRDRRERL RQLALETIDI NKDPYFMKNH LGSYECKLCL TLHNNEGSYL AHTQGKKHQT NLARRAAKE AKEAPAQPAP EKVKVEVKKF VKIGRPGYKV TKQRDSEMGQ QSLLFQIDYP EIAEGIMPRH RFMSAYEQRI E PPDRRWQY LLMAAEPYET IAFKVPSREI DKAEGKFWTH WNRETKQFFL QFHFKMEKPP APPSLPAGPP GVKRPPPPLM NG LPPRPPL PESLPPPPPG GLPLPPMPPT GPAPSGPPGP PQLPPPAPGV HPPAPVVHPP ASGVHPPAPG VHPPAPGVHP PAP GVHPPT SGVHPPAPGV HPPAPGVHPP APGVHPPAPG VHPPAPGVHP PPSAGVHPQA PGVHPAAPAV HPQAPGVHPP APGM HPQAP GVHPQPPGVH PSAPGVHPQP PGVHPSNPGV HPPTPMPPML RPPLPSEGPG NIPPPPPTN

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Macromolecule #3: Splicing factor 3A subunit 3

MacromoleculeName: Splicing factor 3A subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (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

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Macromolecule #4: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (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

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Macromolecule #5: Splicing factor 3B subunit 2

MacromoleculeName: Splicing factor 3B subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (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

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Macromolecule #6: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (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

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Macromolecule #7: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 10.149369 KDa
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

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Macromolecule #8: Splicing factor 3B subunit 6

MacromoleculeName: Splicing factor 3B subunit 6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 14.6069 KDa
SequenceString:
MAMQAAKRAN IRLPPEVNRI LYIRNLPYKI TAEEMYDIFG KYGPIRQIRV GNTPETRGTA YVVYEDIFDA KNACDHLSGF NVCNRYLVV LYYNANRAFQ KMDTKKKEEQ LKLLKEKYGI NTDPPK

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Macromolecule #9: PHD finger-like domain-containing protein 5A

MacromoleculeName: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 12.427524 KDa
SequenceString:
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIV NLGSSKTDLF YERKKYGFKK R

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Macromolecule #2: U2 snRNA

MacromoleculeName: U2 snRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: human (human)
Molecular weightTheoretical: 60.228523 KDa
SequenceString: AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUG(PSU)AG(PSU)A(PSU)(OMC) (PSU)G(PSU)(PSU)CU(OMU)A U CAGU(PSU)UAA(PSU)A U(OMC)UGAUACGU CCUCUAUCCG AGGACAAUAU AUUAAAUGGA UUUUUGGAGC AGGGAGA UG GAAUAGGAGC ...String:
AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUG(PSU)AG(PSU)A(PSU)(OMC) (PSU)G(PSU)(PSU)CU(OMU)A U CAGU(PSU)UAA(PSU)A U(OMC)UGAUACGU CCUCUAUCCG AGGACAAUAU AUUAAAUGGA UUUUUGGAGC AGGGAGA UG GAAUAGGAGC UUGCUCCGUC CACUCCACGC AUCGACCUGG UAUUGCAGUA CCUCCAGGAA CGGUGCACCC

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Macromolecule #10: BPS oligo

MacromoleculeName: BPS oligo / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.395286 KDa
SequenceString:
CAGAUACUAA CACUUGA

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 285 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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 - 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 15681 / Average exposure time: 1.0 sec. / Average electron dose: 52.03 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1470005
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) / Software - details: Ab-initio reconstruction
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 158286
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7q3l

chain_id: A

7q3l

chain_id: B

7q3l

chain_id: C

7q3l

chain_id: E

3lqv

chain_id: F, residue_range: 12-101

7q3l

chain_id: G

7abh

chain_id: 1, residue_range: 42-85

7q3l

chain_id: 2

7q3l

chain_id: 9
RefinementSpace: RECIPROCAL
Output model

PDB-7q4o:
Substrate-bound A-like U2 snRNP

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