EMDB-53554: Cryo-EM structure of the human pre-Bact-OTS complex (whole map)

Basic information

Entry

Database: EMDB / ID: EMD-53554

• Title: Cryo-EM structure of the human pre-Bact-OTS complex (whole map)

Sample

• Complex: pre-Bact-OTS-complex
  • RNA: x 3 types
  • Protein or peptide: x 14 types
• Ligand: x 1 types

• Keywords: spliceosome / SPLICING

Function / homology

Function:

microfibril / regulation of retinoic acid receptor signaling pathway / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / nuclear retinoic acid receptor binding / pre-mRNA binding / U2-type catalytic step 1 spliceosome / embryonic brain development / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / positive regulation of vitamin D receptor signaling pathway / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA polymerase binding / Notch binding / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type spliceosomal complex / nuclear vitamin D receptor binding / NOTCH4 Intracellular Domain Regulates Transcription / transcription elongation factor activity / RNA Polymerase II Transcription Termination / NOTCH3 Intracellular Domain Regulates Transcription / : / Basigin interactions / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of neurogenesis / nuclear androgen receptor binding / ubiquitin-ubiquitin ligase activity / precatalytic spliceosome / Notch-HLH transcription pathway / WW domain binding / Formation of paraxial mesoderm / ubiquitin-like protein conjugating enzyme binding / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / Prp19 complex / negative regulation of transcription elongation by RNA polymerase II / U5 snRNP / U5 snRNA binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / pre-mRNA intronic binding / U2 snRNA binding / U6 snRNA binding / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / retinoic acid receptor signaling pathway / cellular response to retinoic acid / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / acrosomal vesicle / positive regulation of protein export from nucleus / positive regulation of RNA splicing / nuclear receptor binding / helicase activity / protein localization to plasma membrane / spliceosomal complex / transcription coregulator activity / response to cocaine / positive regulation of transcription elongation by RNA polymerase II / sperm end piece / Downregulation of SMAD2/3:SMAD4 transcriptional activity / mRNA splicing, via spliceosome / positive regulation of protein import into nucleus / RING-type E3 ubiquitin transferase / Golgi lumen / Pre-NOTCH Transcription and Translation / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / mRNA processing / nuclear matrix / protein tag activity / calcium-dependent protein binding / protein polyubiquitination / rRNA processing / osteoblast differentiation / transcription corepressor activity / ubiquitin protein ligase activity / single-stranded DNA binding / protein folding / sperm principal piece / microtubule cytoskeleton / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / RNA helicase activity / nuclear speck / cilium

Domain/homology:

WW domain binding protein 11 / WW domain binding protein 11 / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / Ubiquitin-like modifier Hub1/Ubl5 / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / Transcription elongation regulator 1-like / : / PRP38 family / TCERG1 WW domain / FF domain / : / RBM22 CCCH zinc finger domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Pre-mRNA-processing factor 17 / G10 protein signature 2. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / G10 protein signature 1. / : / STL11, N-terminal / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / Pre-mRNA-splicing factor BUD31 / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / : / Winged Helix-turn-helix domain / Sec63 Brl domain / U-box domain profile. / Zinc finger, CCCH-type superfamily / : / zinc finger / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Modified RING finger domain / U-box domain / Sec63 domain / Sec63 Brl domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / WW domain / WW/rsp5/WWP domain signature. / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / WW domain superfamily / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / EF-G domain III/V-like / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease

Component:

Transcription elongation regulator 1 / Pre-mRNA-processing factor 17 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Protein BUD31 homolog / Microfibrillar-associated protein 1 / RING-type E3 ubiquitin-protein ligase PPIL2 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor 38A / Zinc finger matrin-type protein 2 / Ubiquitin-like protein 5 / Pre-mRNA-splicing factor RBM22 / WW domain-binding protein 11

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.12 Å
• Authors: Zhang Z / Kumar V / Zhong J / Dybkov O / Kastner B / Urlaub H / Luhrmann R

Funding support

Germany, 1 items

Organization	Grant number	Country
German Research Foundation (DFG)		Germany

• Citation: Journal: To Be Published; Title: cryo-EM structure of the human pre-Bact-OTS complex; Authors: Zhang Z / Kumar V / Dybkov O / Zhong J / Kastner B / Henning U / Luehrmann R

History

Deposition	May 4, 2025	-
Header (metadata) release	May 13, 2026	-
Map release	May 13, 2026	-
Update	May 13, 2026	-
Current status	May 13, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_53554.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.35 Å

Density

Contour Level	By AUTHOR: 0.055
Minimum - Maximum	-0.16490501 - 0.35897565
Average (Standard dev.)	0.00032380907 (±0.012297201)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 540.0 Å α=β=γ: 90.0 °

Supplemental data

Half map: #2

• File: emd_53554_half_map_1.map

Half map: #1

• File: emd_53554_half_map_2.map

Sample components

Entire : pre-Bact-OTS-complex

• Entire: Name: pre-Bact-OTS-complex

Components

• Complex: pre-Bact-OTS-complex
  • RNA: U5 snRNA
  • RNA: U6 snRNA
  • Protein or peptide: U5 small nuclear ribonucleoprotein 200 kDa helicase
  • Protein or peptide: 116 kDa U5 small nuclear ribonucleoprotein component
  • Protein or peptide: Pre-mRNA-splicing factor 38A
  • Protein or peptide: Microfibrillar-associated protein 1
  • Protein or peptide: Protein BUD31 homolog
  • Protein or peptide: Transcription elongation regulator 1
  • Protein or peptide: WW domain-binding protein 11
  • RNA: pre-mRNA
  • Protein or peptide: Ubiquitin-like protein 5
  • Protein or peptide: Zinc finger matrin-type protein 2
  • Protein or peptide: Pre-mRNA-processing factor 17
  • Protein or peptide: Pre-mRNA-processing-splicing factor 8
  • Protein or peptide: Pre-mRNA-splicing factor RBM22
  • Protein or peptide: RING-type E3 ubiquitin-protein ligase PPIL2
  • Protein or peptide: SNW domain-containing protein 1
• Ligand: INOSITOL HEXAKISPHOSPHATE

Supramolecule #1: pre-Bact-OTS-complex

• Supramolecule: Name: pre-Bact-OTS-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: U5 snRNA

• Macromolecule: Name: U5 snRNA / type: rna / ID: 1 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 24.496414 KDa

Sequence

String:

ACUCUGGUUU CUCUUCAGAU CGCAUAAAUC UUUCGCCUUU UACUAAAGAU UUCCGUGGAG AGGAACAACU CUGAGUC

Macromolecule #2: U6 snRNA

• Macromolecule: Name: U6 snRNA / type: rna / ID: 2 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 27.447449 KDa

Sequence

String:

GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAA

Macromolecule #10: pre-mRNA

• Macromolecule: Name: pre-mRNA / type: rna / ID: 10 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 9.307604 KDa

Sequence

String:

GCCGCCAAGG UAUGUAUCAA GCUUACAAG

Macromolecule #3: U5 small nuclear ribonucleoprotein 200 kDa helicase

• Macromolecule: Name: U5 small nuclear ribonucleoprotein 200 kDa helicase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 244.823422 KDa

Sequence

String:

MADVTARSLQ YEYKANSNLV LQADRSLIDR TRRDEPTGEV LSLVGKLEGT RMGDKAQRTK PQMQEERRAK RRKRDEDRHD INKMKGYTL LSEGIDEMVG IIYKPKTKET RETYEVLLSF IQAALGDQPR DILCGAADEV LAVLKNEKLR DKERRKEIDL L LGQTDDTR YHVLVNLGKK ITDYGGDKEI QNMDDNIDET YGVNVQFESD EEEGDEDVYG EVREEASDDD MEGDEAVVRC TL SANLVAS GELMSSKKKD LHPRDIDAFW LQRQLSRFYD DAIVSQKKAD EVLEILKTAS DDRECENQLV LLLGFNTFDF IKV LRQHRM MILYCTLLAS AQSEAEKERI MGKMEADPEL SKFLYQLHET EKEDLIREER SRRERVRQSR MDTDLETMDL DQGG EALAP RQVLDLEDLV FTQGSHFMAN KRCQLPDGSF RRQRKGYEEV HVPALKPKPF GSEEQLLPVE KLPKYAQAGF EGFKT LNRI QSKLYRAALE TDENLLLCAP TGAGKTNVAL MCMLREIGKH INMDGTINVD DFKIIYIAPM RSLVQEMVGS FGKRLA TYG ITVAELTGDH QLCKEEISAT QIIVCTPEKW DIITRKGGER TYTQLVRLII LDEIHLLHDD RGPVLEALVA RAIRNIE MT QEDVRLIGLS ATLPNYEDVA TFLRVDPAKG LFYFDNSFRP VPLEQTYVGI TEKKAIKRFQ IMNEIVYEKI MEHAGKNQ V LVFVHSRKET GKTARAIRDM CLEKDTLGLF LREGSASTEV LRTEAEQCKN LELKDLLPYG FAIHHAGMTR VDRTLVEDL FADKHIQVLV STATLAWGVN LPAHTVIIKG TQVYSPEKGR WTELGALDIL QMLGRAGRPQ YDTKGEGILI TSHGELQYYL SLLNQQLPI ESQMVSKLPD MLNAEIVLGN VQNAKDAVNW LGYAYLYIRM LRSPTLYGIS HDDLKGDPLL DQRRLDLVHT A ALMLDKNN LVKYDKKTGN FQVTELGRIA SHYYITNDTV QTYNQLLKPT LSEIELFRVF SLSSEFKNIT VREEEKLELQ KL LERVPIP VKESIEEPSA KINVLLQAFI SQLKLEGFAL MADMVYVTQS AGRLMRAIFE IVLNRGWAQL TDKTLNLCKM IDK RMWQSM CPLRQFRKLP EEVVKKIEKK NFPFERLYDL NHNEIGELIR MPKMGKTIHK YVHLFPKLEL SVHLQPITRS TLKV ELTIT PDFQWDEKVH GSSEAFWILV EDVDSEVILH HEYFLLKAKY AQDEHLITFF VPVFEPLPPQ YFIRVVSDRW LSCET QLPV SFRHLILPEK YPPPTELLDL QPLPVSALRN SAFESLYQDK FPFFNPIQTQ VFNTVYNSDD NVFVGAPTGS GKTICA EFA ILRMLLQSSE GRCVYITPME ALAEQVYMDW YEKFQDRLNK KVVLLTGETS TDLKLLGKGN IIISTPEKWD ILSRRWK QR KNVQNINLFV VDEVHLIGGE NGPVLEVICS RMRYISSQIE RPIRIVALSS SLSNAKDVAH WLGCSATSTF NFHPNVRP V PLELHIQGFN ISHTQTRLLS MAKPVYHAIT KHSPKKPVIV FVPSRKQTRL TAIDILTTCA ADIQRQRFLH CTEKDLIPY LEKLSDSTLK ETLLNGVGYL HEGLSPMERR LVEQLFSSGA IQVVVASRSL CWGMNVAAHL VIIMDTQYYN GKIHAYVDYP IYDVLQMVG HANRPLQDDE GRCVIMCQGS KKDFFKKFLY EPLPVESHLD HCMHDHFNAE IVTKTIENKQ DAVDYLTWTF L YRRMTQNP NYYNLQGISH RHLSDHLSEL VEQTLSDLEQ SKCISIEDEM DVAPLNLGMI AAYYYINYTT IELFSMSLNA KT KVRGLIE IISNAAEYEN IPIRHHEDNL LRQLAQKVPH KLNNPKFNDP HVKTNLLLQA HLSRMQLSAE LQSDTEEILS KAI RLIQAC VDVLSSNGWL SPALAAMELA QMVTQAMWSK DSYLKQLPHF TSEHIKRCTD KGVESVFDIM EMEDEERNAL LQLT DSQIA DVARFCNRYP NIELSYEVVD KDSIRSGGPV VVLVQLEREE EVTGPVIAPL FPQKREEGWW VVIGDAKSNS LISIK RLTL QQKAKVKLDF VAPATGAHNY TLYFMSDAYM GCDQEYKFSV DVKEAETDSD SD

UniProtKB: U5 small nuclear ribonucleoprotein 200 kDa helicase

Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component

• Macromolecule: Name: 116 kDa U5 small nuclear ribonucleoprotein component / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 109.560625 KDa

Sequence

String:

MDTDLYDEFG NYIGPELDSD EDDDELGRET KDLDEMDDDD DDDDVGDHDD DHPGMEVVLH EDKKYYPTAE EVYGPEVETI VQEEDTQPL TEPIIKPVKT KKFTLMEQTL PVTVYEMDFL ADLMDNSELI RNVTLCGHLH HGKTCFVDCL IEQTHPEIRK R YDQDLCYT DILFTEQERG VGIKSTPVTV VLPDTKGKSY LFNIMDTPGH VNFSDEVTAG LRISDGVVLF IDAAEGVMLN TE RLIKHAV QERLAVTVCI NKIDRLILEL KLPPTDAYYK LRHIVDEVNG LISMYSTDEN LILSPLLGNV CFSSSQYSIC FTL GSFAKI YADTFGDINY QEFAKRLWGD IYFNPKTRKF TKKAPTSSSQ RSFVEFILEP LYKILAQVVG DVDTSLPRTL DELG IHLTK EELKLNIRPL LRLVCKKFFG EFTGFVDMCV QHIPSPKVGA KPKIEHTYTG GVDSDLGEAM SDCDPDGPLM CHTTK MYST DDGVQFHAFG RVLSGTIHAG QPVKVLGENY TLEDEEDSQI CTVGRLWISV ARYHIEVNRV PAGNWVLIEG VDQPIV KTA TITEPRGNEE AQIFRPLKFN TTSVIKIAVE PVNPSELPKM LDGLRKVNKS YPSLTTKVEE SGEHVILGTG ELYLDCV MH DLRKMYSEID IKVADPVVTF CETVVETSSL KCFAETPNKK NKITMIAEPL EKGLAEDIEN EVVQITWNRK KLGEFFQT K YDWDLLAARS IWAFGPDATG PNILVDDTLP SEVDKALLGS VKDSIVQGFQ WGTREGPLCD ELIRNVKFKI LDAVVAQEP LHRGGGQIIP TARRVVYSAF LMATPRLMEP YYFVEVQAPA DCVSAVYTVL ARRRGHVTQD APIPGSPLYT IKAFIPAIDS FGFETDLRT HTQGQAFSLS VFHHWQIVPG DPLDKSIVIR PLEPQPAPHL AREFMIKTRR RKGLSEDVSI SKFFDDPMLL E LAKQDVVL NYPM

UniProtKB: 116 kDa U5 small nuclear ribonucleoprotein component

Macromolecule #5: Pre-mRNA-splicing factor 38A

• Macromolecule: Name: Pre-mRNA-splicing factor 38A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 37.563863 KDa

Sequence

String:

MANRTVKDAH SIHGTNPQYL VEKIIRTRIY ESKYWKEECF GLTAELVVDK AMELRFVGGV YGGNIKPTPF LCLTLKMLQI QPEKDIIVE FIKNEDFKYV RMLGALYMRL TGTAIDCYKY LEPLYNDYRK IKSQNRNGEF ELMHVDEFID ELLHSERVCD I ILPRLQKR YVLEEAEQLE PRVSALEEDM DDVESSEEEE EEDEKLERVP SPDHRRRSYR DLDKPRRSPT LRYRRSRSRS PR RRSRSPK RRSPSPRRER HRSKSPRRHR SRSRDRRHRS RSKSPGHHRS HRHRSHSKSP ERSKKSHKKS RRGNE

UniProtKB: Pre-mRNA-splicing factor 38A

Macromolecule #6: Microfibrillar-associated protein 1

• Macromolecule: Name: Microfibrillar-associated protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 52.050527 KDa

Sequence

String:

MSVPSALMKQ PPIQSTAGAV PVRNEKGEIS MEKVKVKRYV SGKRPDYAPM ESSDEEDEEF QFIKKAKEQE AEPEEQEEDS SSDPRLRRL QNRISEDVEE RLARHRKIVE PEVVGESDSE VEGDAWRMER EDSSEEEEEE IDDEEIERRR GMMRQRAQER K NEEMEVME VEDEGRSGEE SESESEYEEY TDSEDEMEPR LKPVFIRKKD RVTVQEREAE ALKQKELEQE AKRMAEERRK YT LKIVEEE TKKELEENKR SLAALDALNT DDENDEEEYE AWKVRELKRI KRDREDREAL EKEKAEIERM RNLTEEERRA ELR ANGKVI TNKAVKGKYK FLQKYYHRGA FFMDEDEEVY KRDFSAPTLE DHFNKTILPK VMQVKNFGRS GRTKYTHLVD QDTT SFDSA WGQESAQNTK FFKQKAAGVR DVFERPSAKK RKTT

UniProtKB: Microfibrillar-associated protein 1

Macromolecule #7: Protein BUD31 homolog

• Macromolecule: Name: Protein BUD31 homolog / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 17.03285 KDa

Sequence

String:

MPKVKRSRKA PPDGWELIEP TLDELDQKMR EAETEPHEGK RKVESLWPIF RIHHQKTRYI FDLFYKRKAI SRELYEYCIK EGYADKNLI AKWKKQGYEN LCCLRCIQTR DTNFGTNCIC RVPKSKLEVG RIIECTHCGC RGCSG

UniProtKB: Protein BUD31 homolog

Macromolecule #8: Transcription elongation regulator 1

• Macromolecule: Name: Transcription elongation regulator 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 124.083 KDa

Sequence

String:

MAERGGDGGE SERFNPGELR MAQQQALRFR GPAPPPNAVM RGPPPLMRPP PPFGMMRGPP PPPRPPFGRP PFDPNMPPMP PPGGIPPPM GPPHLQRPPF MPPPMSSMPP PPGMMFPPGM PPVTAPGTPA LPPTEEIWVE NKTPDGKVYY YNARTRESAW T KPDGVKVI QQSELTPMLA AQAQVQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQAQAQAQAQ AQ AQVQAQV QAQVQAQAVG ASTPTTSSPA PAVSTSTSSS TPSSTTSTTT TATSVAQTVS TPTTQDQTPS SAVSVATPTV SVS TPAPTA TPVQTVPQPH PQTLPPAVPH SVPQPTTAIP AFPPVMVPPF RVPLPGMPIP LPGVAMMQIV SCPYVKTVAT TKTG VLPGM APPIVPMIHP QVAIAASPAT LAGATAVSEW TEYKTADGKT YYYNNRTLES TWEKPQELKE KEKLEEKIKE PIKEP SEEP LPMETEEEDP KEEPIKEIKE EPKEEEMTEE EKAAQKAKPV ATAPIPGTPW CVVWTGDERV FFYNPTTRLS MWDRPD DLI GRADVDKIIQ EPPHKKGMEE LKKLRHPTPT MLSIQKWQFS MSAIKEEQEL MEEINEDEPV KAKKRKRDDN KDIDSEK EA AMEAEIKAAR ERAIVPLEAR MKQFKDMLLE RGVSAFSTWE KELHKIVFDP RYLLLNPKER KQVFDQYVKT RAEEERRE K KNKIMQAKED FKKMMEEAKF NPRATFSEFA AKHAKDSRFK AIEKMKDREA LFNEFVAAAR KKEKEDSKTR GEKIKSDFF ELLSNHHLDS QSRWSKVKDK VESDPRYKAV DSSSMREDLF KQYIEKIAKN LDSEKEKELE RQARIEASLR EREREVQKAR SEQTKEIDR EREQHKREEA IQNFKALLSD MVRSSDVSWS DTRRTLRKDH RWESGSLLER EEKEKLFNEH IEALTKKKRE H FRQLLDET SAITLTSTWK EVKKIIKEDP RCIKFSSSDR KKQREFEEYI RDKYITAKAD FRTLLKETKF ITYRSKKLIQ ES DQHLKDV EKILQNDKRY LVLDCVPEER RKLIVAYVDD LDRRGPPPPP TASEPTRRST K

UniProtKB: Transcription elongation regulator 1

Macromolecule #9: WW domain-binding protein 11

• Macromolecule: Name: WW domain-binding protein 11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 70.098641 KDa

Sequence

String:

MGRRSTSSTK SGKFMNPTDQ ARKEARKREL KKNKKQRMMV RAAVLKMKDP KQIIRDMEKL DEMEFNPVQQ PQLNEKVLKD KRKKLRETF ERILRLYEKE NPDIYKELRK LEVEYEQKRA QLSQYFDAVK NAQHVEVESI PLPDMPHAPS NILIQDIPLP G AQPPSILK KTSAYGPPTR AVSILPLLGH GVPRLPPGRK PPGPPPGPPP PQVVQMYGRK VGFALDLPPR RRDEDMLYSP EL AQRGHDD DVSSTSEDDG YPEDMDQDKH DDSTDDSDTD KSDGESDGDE FVHRDNGERD NNEEKKSGLS VRFADMPGKS RKK KKNMKE LTPLQAMMLR MAGQEIPEEG REVEEFSEDD DEDDSDDSEA EKQSQKQHKE ESHSDGTSTA SSQQQAPPQS VPPS QIQAP PMPGPPPLGP PPAPPLRPPG PPTGLPPGPP PGAPPFLRPP GMPGLRGPLP RLLPPGPPPG RPPGPPPGPP PGLPP GPPP RGPPPRLPPP APPGIPPPRP GMMRPPLVPP LGPAPPGLFP PAPLPNPGVL SAPPNLIQRP KADDTSAATI EKKATA TIS AKPQITNPKA EITRFVPTAL RVRRENKGAT AAPQRKSEDD SAVPLAKAAP KSGPSVPVSV QTKDDVYEAF MKEMEGL L

UniProtKB: WW domain-binding protein 11

Macromolecule #11: Ubiquitin-like protein 5

• Macromolecule: Name: Ubiquitin-like protein 5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 8.560945 KDa

Sequence

String:

MIEVVCNDRL GKKVRVKCNT DDTIGDLKKL IAAQTGTRWN KIVLKKWYTI FKDHVSLGDY EIHDGMNLEL YYQ

UniProtKB: Ubiquitin-like protein 5

Macromolecule #12: Zinc finger matrin-type protein 2

• Macromolecule: Name: Zinc finger matrin-type protein 2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 23.664047 KDa

Sequence

String:

MASGSGTKNL DFRRKWDKDE YEKLAEKRLT EEREKKDGKP VQPVKRELLR HRDYKVDLES KLGKTIVITK TTPQSEMGGY YCNVCDCVV KDSINFLDHI NGKKHQRNLG MSMRVERSTL DQVKKRFEVN KKKMEEKQKD YDFEERMKEL REEEEKAKAY K KEKQKEKK RRAEEDLTFE EDDEMAAVMG FSGFGSTKKS Y

UniProtKB: Zinc finger matrin-type protein 2

Macromolecule #13: Pre-mRNA-processing factor 17

• Macromolecule: Name: Pre-mRNA-processing factor 17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 65.61218 KDa

Sequence

String:

MSAAIAALAA SYGSGSGSES DSDSESSRCP LPAADSLMHL TKSPSSKPSL AVAVDSAPEV AVKEDLETGV HLDPAVKEVQ YNPTYETMF APEFGPENPF RTQQMAAPRN MLSGYAEPAH INDFMFEQQR RTFATYGYAL DPSLDNHQVS AKYIGSVEEA E KNQGLTVF ETGQKKTEKR KKFKENDASN IDGFLGPWAK YVDEKDVAKP SEEEQKELDE ITAKRQKKGK QEEEKPGEEK TI LHVKEMY DYQGRSYLHI PQDVGVNLRS TMPPEKCYLP KKQIHVWSGH TKGVSAVRLF PLSGHLLLSC SMDCKIKLWE VYG ERRCLR TFIGHSKAVR DICFNTAGTQ FLSAAYDRYL KLWDTETGQC ISRFTNRKVP YCVKFNPDED KQNLFVAGMS DKKI VQWDI RSGEIVQEYD RHLGAVNTIV FVDENRRFVS TSDDKSLRVW EWDIPVDFKY IAEPSMHSMP AVTLSPNGKW LACQS MDNQ ILIFGAQNRF RLNKKKIFKG HMVAGYACQV DFSPDMSYVI SGDGNGKLNI WDWKTTKLYS RFKAHDKVCI GAVWHP HET SKVITCGWDG LIKLWD

UniProtKB: Pre-mRNA-processing factor 17

Macromolecule #14: Pre-mRNA-processing-splicing factor 8

• Macromolecule: Name: Pre-mRNA-processing-splicing factor 8 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 273.97425 KDa

Sequence

String:

MAGVFPYRGP GNPVPGPLAP LPDYMSEEKL QEKARKWQQL QAKRYAEKRK FGFVDAQKED MPPEHVRKII RDHGDMTNRK FRHDKRVYL GALKYMPHAV LKLLENMPMP WEQIRDVPVL YHITGAISFV NEIPWVIEPV YISQWGSMWI MMRREKRDRR H FKRMRFPP FDDEEPPLDY ADNILDVEPL EAIQLELDPE EDAPVLDWFY DHQPLRDSRK YVNGSTYQRW QFTLPMMSTL YR LANQLLT DLVDDNYFYL FDLKAFFTSK ALNMAIPGGP KFEPLVRDIN LQDEDWNEFN DINKIIIRQP IRTEYKIAFP YLY NNLPHH VHLTWYHTPN VVFIKTEDPD LPAFYFDPLI NPISHRHSVK SQEPLPDDDE EFELPEFVEP FLKDTPLYTD NTAN GIALL WAPRPFNLRS GRTRRALDIP LVKNWYREHC PAGQPVKVRV SYQKLLKYYV LNALKHRPPK AQKKRYLFRS FKATK FFQS TKLDWVEVGL QVCRQGYNML NLLIHRKNLN YLHLDYNFNL KPVKTLTTKE RKKSRFGNAF HLCREVLRLT KLVVDS HVQ YRLGNVDAFQ LADGLQYIFA HVGQLTGMYR YKYKLMRQIR MCKDLKHLIY YRFNTGPVGK GPGCGFWAAG WRVWLFF MR GITPLLERWL GNLLARQFEG RHSKGVAKTV TKQRVESHFD LELRAAVMHD ILDMMPEGIK QNKARTILQH LSEAWRCW K ANIPWKVPGL PTPIENMILR YVKAKADWWT NTAHYNRERI RRGATVDKTV CKKNLGRLTR LYLKAEQERQ HNYLKDGPY ITAEEAVAVY TTTVHWLESR RFSPIPFPPL SYKHDTKLLI LALERLKEAY SVKSRLNQSQ REELGLIEQA YDNPHEALSR IKRHLLTQR AFKEVGIEFM DLYSHLVPVY DVEPLEKITD AYLDQYLWYE ADKRRLFPPW IKPADTEPPP LLVYKWCQGI N NLQDVWET SEGECNVMLE SRFEKMYEKI DLTLLNRLLR LIVDHNIADY MTAKNNVVIN YKDMNHTNSY GIIRGLQFAS FI VQYYGLV MDLLVLGLHR ASEMAGPPQM PNDFLSFQDI ATEAAHPIRL FCRYIDRIHI FFRFTADEAR DLIQRYLTEH PDP NNENIV GYNNKKCWPR DARMRLMKHD VNLGRAVFWD IKNRLPRSVT TVQWENSFVS VYSKDNPNLL FNMCGFECRI LPKC RTSYE EFTHKDGVWN LQNEVTKERT AQCFLRVDDE SMQRFHNRVR QILMASGSTT FTKIVNKWNT ALIGLMTYFR EAVVN TQEL LDLLVKCENK IQTRIKIGLN SKMPSRFPPV VFYTPKELGG LGMLSMGHVL IPQSDLRWSK QTDVGITHFR SGMSHE EDQ LIPNLYRYIQ PWESEFIDSQ RVWAEYALKR QEAIAQNRRL TLEDLEDSWD RGIPRINTLF QKDRHTLAYD KGWRVRT DF KQYQVLKQNP FWWTHQRHDG KLWNLNNYRT DMIQALGGVE GILEHTLFKG TYFPTWEGLF WEKASGFEES MKWKKLTN A QRSGLNQIPN RRFTLWWSPT INRANVYVGF QVQLDLTGIF MHGKIPTLKI SLIQIFRAHL WQKIHESIVM DLCQVFDQE LDALEIETVQ KETIHPRKSY KMNSSCADIL LFASYKWNVS RPSLLADSKD VMDSTTTQKY WIDIQLRWGD YDSHDIERYA RAKFLDYTT DNMSIYPSPT GVLIAIDLAY NLHSAYGNWF PGSKPLIQQA MAKIMKANPA LYVLRERIRK GLQLYSSEPT E PYLSSQNY GELFSNQIIW FVDDTNVYRV TIHKTFEGNL TTKPINGAIF IFNPRTGQLF LKIIHTSVWA GQKRLGQLAK WK TAEEVAA LIRSLPVEEQ PKQIIVTRKG MLDPLEVHLL DFPNIVIKGS ELQLPFQACL KVEKFGDLIL KATEPQMVLF NLY DDWLKT ISSYTAFSRL ILILRALHVN NDRAKVILKP DKTTITEPHH IWPTLTDEEW IKVEVQLKDL ILADYGKKNN VNVA SLTQS EIRDIILGME ISAPSQQRQQ IAEIEKQTKE QSQLTATQTR TVNKHGDEII TSTTSNYETQ TFSSKTEWRV RAISA ANLH LRTNHIYVSS DDIKETGYTY ILPKNVLKKF ICISDLRAQI AGYLYGVSPP DNPQVKEIRC IVMVPQWGTH QTVHLP GQL PQHEYLKEME PLGWIHTQPN ESPQLSPQDV TTHAKIMADN PSWDGEKTII ITCSFTPGSC TLTAYKLTPS GYEWGRQ NT DKGNNPKGYL PSHYERVQML LSDRFLGFFM VPAQSSWNYN FMGVRHDPNM KYELQLANPK EFYHEVHRPS HFLNFALL Q EGEVYSADRE DLYA

UniProtKB: Pre-mRNA-processing-splicing factor 8

Macromolecule #15: Pre-mRNA-splicing factor RBM22

• Macromolecule: Name: Pre-mRNA-splicing factor RBM22 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 46.959555 KDa

Sequence

String:

MATSLGSNTY NRQNWEDADF PILCQTCLGE NPYIRMTKEK YGKECKICAR PFTVFRWCPG VRMRFKKTEV CQTCSKLKNV CQTCLLDLE YGLPIQVRDA GLSFKDDMPK SDVNKEYYTQ NMEREISNSD GTRPVGMLGK ATSTSDMLLK LARTTPYYKR N RPHICSFW VKGECKRGEE CPYRHEKPTD PDDPLADQNI KDRYYGINDP VADKLLKRAS TMPRLDPPED KTITTLYVGG LG DTITETD LRNHFYQFGE IRTITVVQRQ QCAFIQFATR QAAEVAAEKS FNKLIVNGRR LNVKWGRSQA ARGKEKEKDG TTD SGIKLE PVPGLPGALP PPPAAEEEAS ANYFNLPPSG PPAVVNIALP PPPGIAPPPP PGFGPHMFHP MGPPPPFMRA PGPI HYPSQ DPQRMGAHAG KHSSP

UniProtKB: Pre-mRNA-splicing factor RBM22

Macromolecule #16: RING-type E3 ubiquitin-protein ligase PPIL2

• Macromolecule: Name: RING-type E3 ubiquitin-protein ligase PPIL2 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 58.910379 KDa

Sequence

String:

MGKRQHQKDK MYITCAEYTH FYGGKKPDLP QTNFRRLPFD HCSLSLQPFV YPVCTPDGIV FDLLNIVPWL KKYGTNPSNG EKLDGRSLI KLNFSKNSEG KYHCPVLFTV FTNNTHIVAV RTTGNVYAYE AVEQLNIKAK NFRDLLTDEP FSRQDIITLQ D PTNLDKFN VSNFYHVKNN MKIIDPDEEK AKQDPSYYLK NTNAETRETL QELYKEFKGD EILAATMKAP EKKKVDKLNA AH YSTGKVS ASFTSTAMVP ETTHEAAAID EDVLRYQFVK KKGYVRLHTN KGDLNLELHC DLTPKTCENF IRLCKKHYYD GTI FHRSIR NFVIQGGDPT GTGTGGESYW GKPFKDEFRP NLSHTGRGIL SMANSGPNSN RSQFFITFRS CAYLDKKHTI FGRV VGGFD VLTAMENVES DPKTDRPKEE IRIDATTVFV DPYEEADAQI AQERKTQLKV APETKVKSSQ PQAGSQGPQT FRQGV GKYI NPAATKRAAE EEPSTSATVP MSKKKPSRGF GDFSSW

UniProtKB: RING-type E3 ubiquitin-protein ligase PPIL2

Macromolecule #17: SNW domain-containing protein 1

• Macromolecule: Name: SNW domain-containing protein 1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.326215 KDa

Sequence

String:

MALTSFLPAP TQLSQDQLEA EEKARSQRSR QTSLVSSRRE PPPYGYRKGW IPRLLEDFGD GGAFPEIHVA QYPLDMGRKK KMSNALAIQ VDSEGKIKYD AIARQGQSKD KVIYSKYTDL VPKEVMNADD PDLQRPDEEA IKEITEKTRV ALEKSVSQKV A AAMPVRAA DKLAPAQYIR YTPSQQGVAF NSGAKQRVIR MVEMQKDPME PPRFKINKKI PRGPPSPPAP VMHSPSRKMT VK EQQEWKI PPCISNWKNA KGYTIPLDKR LAADGRGLQT VHINENFAKL AEALYIADRK AREAVEMRAQ VERKMAQKEK EKH EEKLRE MAQKARERRA GIKTHVEKED GEARERDEIR HDRRKERQHD RNLSRAAPDK RSKLQRNENR DISEVIALGV PNPR TSNEV QYDQRLFNQS KGMDSGFAGG EDEIYNVYDQ AWRGGKDMAQ SIYRPSKNLD KDMYGDDLEA RIKTNRFVPD KEFSG SDRR QRGREGPVQF EEDPFGLDKF LEEAKQHGGS KRPSDSSRPK EH

UniProtKB: SNW domain-containing protein 1

Macromolecule #18: INOSITOL HEXAKISPHOSPHATE

• Macromolecule: Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 18 / Number of copies: 1 / Formula: IHP
• Molecular weight: Theoretical: 660.035 Da

Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.9
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: OTHER / Details: ab initio
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 35015
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD