EMDB-11693: Human pre-Bact-2 spliceosome core structure

Basic information

• Entry: Database: EMDB / ID: EMD-11693
• Title: Human pre-Bact-2 spliceosome core structure
• Map data: Masked/sharpened map of the pre-Bact-2 spliceosome core structure.

Sample

• Complex: pre-Bact-2 spliceosomal core structure
  • Complex: pre-Bact-2 spliceosomal core structure
    • Protein or peptide: x 13 types
    • RNA: x 3 types
  • Complex: MINX M3 pre-mRNA
    • RNA: x 1 types
• Ligand: x 3 types

• Keywords: Complex / spliceosome / catalytic activation / splicing

Function / homology

Function:

microfibril / regulation of vitamin D receptor signaling pathway / regulation of retinoic acid receptor signaling pathway / non-collagenous component of basement membrane / U4atac/U6atac x U5 tri-snRNP complex / embryonic brain development / nuclear retinoic acid receptor binding / post-spliceosomal complex / positive regulation of mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / mRNA 3'-end processing / U12-type catalytic step 2 spliceosome / post-mRNA release spliceosomal complex / U12-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / RNA Polymerase II Transcription Termination / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / U2-type spliceosomal complex / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / NOTCH4 Intracellular Domain Regulates Transcription / pre-mRNA binding / U2-type catalytic step 2 spliceosome / positive regulation of neurogenesis / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / NOTCH3 Intracellular Domain Regulates Transcription / U2-type catalytic step 1 spliceosome / positive regulation of protein localization to mitochondrion / mRNA stabilization / mRNA cis splicing, via spliceosome / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / Notch-HLH transcription pathway / Formation of paraxial mesoderm / precatalytic spliceosome / positive regulation of transforming growth factor beta receptor signaling pathway / WD40-repeat domain binding / SMAD binding / mRNA Splicing - Minor Pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Prp19 complex / negative regulation of mRNA splicing, via spliceosome / U5 snRNA binding / spliceosomal tri-snRNP complex assembly / U5 snRNP / U6 snRNA binding / U4/U6 x U5 tri-snRNP complex / Cajal body / retinoic acid receptor signaling pathway / cellular response to retinoic acid / DNA damage checkpoint signaling / spliceosomal snRNP assembly / positive regulation of protein export from nucleus / catalytic step 2 spliceosome / RNA splicing / spliceosomal complex / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / nuclear receptor binding / cellular response to xenobiotic stimulus / response to cocaine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to tumor necrosis factor / positive regulation of protein import into nucleus / mRNA splicing, via spliceosome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / fibrillar center / mRNA processing / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / mRNA Polyadenylation / nuclear matrix / protein tag activity / calcium-dependent protein binding / transcription corepressor activity / cellular response to lipopolysaccharide / nuclear membrane / Dengue Virus-Host Interactions / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / nucleic acid binding / transcription coactivator activity / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / mRNA binding / GTPase activity / regulation of transcription by RNA polymerase II / GTP binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription

Domain/homology:

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 / PRP38 family / : / RBM22 CCCH zinc finger domain / Pre-mRNA-processing factor 17 / G10 protein signature 2. / BUD31/G10-related, conserved site / G10 protein signature 1. / : / STL11, N-terminal / Pre-mRNA-splicing factor Cwc2/Slt11 / SKI-interacting protein SKIP, SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / SKI-interacting protein, SKIP / SKIP/SNW domain / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / pre-mRNA splicing factor component / G10 protein / Pre-mRNA-splicing factor BUD31 / : / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Myb-like DNA-binding domain / Zinc finger, CCCH-type superfamily / zinc finger / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Snu114, GTP-binding domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Myb-type HTH DNA-binding domain profile. / Myb domain / Elongation Factor G, domain II / Elongation Factor G, domain III / Elongation factor G, domain IV / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 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 / 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 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Zinc finger C2H2 superfamily / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Homeobox-like domain superfamily / Small GTP-binding protein domain / Ubiquitin family / Ubiquitin-like domain / WD domain, G-beta repeat / Ribonuclease H-like superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily

Component:

Pleiotropic regulator 1 / Pre-mRNA-processing factor 17 / Protein BUD31 homolog / Microfibrillar-associated protein 1 / 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 / Cell division cycle 5-like protein / Ubiquitin-like protein 5 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog

• Biological species: Homo sapiens (human) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 4.2 Å
• Authors: Townsend C / Kastner B

Funding support

Germany, 1 items

Organization	Grant number	Country
German Research Foundation (DFG)	860	Germany

• Citation: Journal: Science / Year: 2020; Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.; Authors: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / ; Abstract: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.

History

Deposition	Sep 4, 2020	-
Header (metadata) release	Dec 9, 2020	-
Map release	Dec 9, 2020	-
Update	Oct 1, 2025	-
Current status	Oct 1, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11693.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Masked/sharpened map of the pre-Bact-2 spliceosome core structure.
• Voxel size: X=Y=Z: 1.16 Å

Density

Contour Level	By AUTHOR: 0.051 / Movie #1: 0.051
Minimum - Maximum	-0.06758506 - 0.13364817
Average (Standard dev.)	0.00027001693 (±0.0034261802)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 445.44 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.16	1.16	1.16
M x/y/z	384	384	384
origin x/y/z	0.000	0.000	0.000
length x/y/z	445.440	445.440	445.440
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	240	240	240
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	384	384	384
D min/max/mean	-0.068	0.134	0.000

Supplemental data

Sample components

Entire : pre-Bact-2 spliceosomal core structure

• Entire: Name: pre-Bact-2 spliceosomal core structure

Components

• Complex: pre-Bact-2 spliceosomal core structure
  • Complex: pre-Bact-2 spliceosomal core structure
    • Protein or peptide: 116 kDa U5 small nuclear ribonucleoprotein component
    • Protein or peptide: Protein BUD31 homolog
    • Protein or peptide: Cell division cycle 5-like protein
    • Protein or peptide: Spliceosome-associated protein CWC15 homolog
    • Protein or peptide: Microfibrillar-associated protein 1
    • Protein or peptide: Pleiotropic regulator 1
    • Protein or peptide: Pre-mRNA-processing factor 17
    • Protein or peptide: Pre-mRNA-splicing factor 38A
    • Protein or peptide: Pre-mRNA-processing-splicing factor 8
    • Protein or peptide: Pre-mRNA-splicing factor RBM22
    • Protein or peptide: SNW domain-containing protein 1
    • Protein or peptide: Zinc finger matrin-type protein 2
    • RNA: U2 snRNA
    • RNA: U5 snRNA
    • RNA: U6 snRNA
    • Protein or peptide: Ubiquitin-like protein 5
  • Complex: MINX M3 pre-mRNA
    • RNA: MINX M3 pre-mRNA
• Ligand: GUANOSINE-5'-TRIPHOSPHATE
• Ligand: MAGNESIUM ION
• Ligand: D-chiro inositol hexakisphosphate

Supramolecule #1: pre-Bact-2 spliceosomal core structure

• Supramolecule: Name: pre-Bact-2 spliceosomal core structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17

Supramolecule #2: pre-Bact-2 spliceosomal core structure

• Supramolecule: Name: pre-Bact-2 spliceosomal core structure / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6, #8-#17
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #3: MINX M3 pre-mRNA

• Supramolecule: Name: MINX M3 pre-mRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
• Source (natural): Organism: synthetic construct (others)

Macromolecule #1: 116 kDa U5 small nuclear ribonucleoprotein component

• Macromolecule: Name: 116 kDa U5 small nuclear ribonucleoprotein component / type: protein_or_peptide / ID: 1 / 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 #2: Protein BUD31 homolog

• Macromolecule: Name: Protein BUD31 homolog / type: protein_or_peptide / ID: 2 / 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 #3: Cell division cycle 5-like protein

• Macromolecule: Name: Cell division cycle 5-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 92.406883 KDa

Sequence

String:

MPRIMIKGGV WRNTEDEILK AAVMKYGKNQ WSRIASLLHR KSAKQCKARW YEWLDPSIKK TEWSREEEEK LLHLAKLMPT QWRTIAPII GRTAAQCLEH YEFLLDKAAQ RDNEEETTDD PRKLKPGEID PNPETKPARP DPIDMDEDEL EMLSEARARL A NTQGKKAK RKAREKQLEE ARRLAALQKR RELRAAGIEI QKKRKRKRGV DYNAEIPFEK KPALGFYDTS EENYQALDAD FR KLRQQDL DGELRSEKEG RDRKKDKQHL KRKKESDLPS AILQTSGVSE FTKKRSKLVL PAPQISDAEL QEVVKVGQAS EIA RQTAEE SGITNSASST LLSEYNVTNN SVALRTPRTP ASQDRILQEA QNLMALTNVD TPLKGGLNTP LHESDFSGVT PQRQ VVQTP NTVLSTPFRT PSNGAEGLTP RSGTTPKPVI NSTPGRTPLR DKLNINPEDG MADYSDPSYV KQMERESREH LRLGL LGLP APKNDFEIVL PENAEKELEE REIDDTYIED AADVDARKQA IRDAERVKEM KRMHKAVQKD LPRPSEVNET ILRPLN VEP PLTDLQKSEE LIKKEMITML HYDLLHHPYE PSGNKKGKTV GFGTNNSEHI TYLEHNPYEK FSKEELKKAQ DVLVQEM EV VKQGMSHGEL SSEAYNQVWE ECYSQVLYLP GQSRYTRANL ASKKDRIESL EKRLEINRGH MTTEAKRAAK MEKKMKIL L GGYQSRAMGL MKQLNDLWDQ IEQAHLELRT FEELKKHEDS AIPRRLECLK EDVQRQQERE KELQHRYADL LLEKETLKS KF

UniProtKB: Cell division cycle 5-like protein

Macromolecule #4: Spliceosome-associated protein CWC15 homolog

• Macromolecule: Name: Spliceosome-associated protein CWC15 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 26.674447 KDa

Sequence

String:

MTTAARPTFE PARGGRGKGE GDLSQLSKQY SSRDLPSHTK IKYRQTTQDA PEEVRNRDFR RELEERERAA AREKNRDRPT REHTTSSSV SKKPRLDQIP AANLDADDPL TDEEDEDFEE ESDDDDTAAL LAELEKIKKE RAEEQARKEQ EQKAEEERIR M ENILSGNP LLNLTGPSQP QANFKVKRRW DDDVVFKNCA KGVDDQKKDK RFVNDTLRSE FHKKFMEKYI K

UniProtKB: Spliceosome-associated protein CWC15 homolog

Macromolecule #5: Microfibrillar-associated protein 1

• Macromolecule: Name: Microfibrillar-associated protein 1 / type: protein_or_peptide / ID: 5 / 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 #6: Pleiotropic regulator 1

• Macromolecule: Name: Pleiotropic regulator 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 57.280758 KDa

Sequence

String:

MVEEVQKHSV HTLVFRSLKR THDMFVADNG KPVPLDEESH KRKMAIKLRN EYGPVLHMPT SKENLKEKGP QNATDSYVHK QYPANQGQE VEYFVAGTHP YPPGPGVALT ADTKIQRMPS ESAAQSLAVA LPLQTKADAN RTAPSGSEYR HPGASDRPQP T AMNSIVME TGNTKNSALM AKKAPTMPKP QWHPPWKLYR VISGHLGWVR CIAVEPGNQW FVTGSADRTI KIWDLASGKL KL SLTGHIS TVRGVIVSTR SPYLFSCGED KQVKCWDLEY NKVIRHYHGH LSAVYGLDLH PTIDVLVTCS RDSTARIWDV RTK ASVHTL SGHTNAVATV RCQAAEPQII TGSHDTTIRL WDLVAGKTRV TLTNHKKSVR AVVLHPRHYT FASGSPDNIK QWKF PDGSF IQNLSGHNAI INTLTVNSDG VLVSGADNGT MHLWDWRTGY NFQRVHAAVQ PGSLDSESGI FACAFDQSES RLLTA EADK TIKVYREDDT ATEETHPVSW KPEIIKRKRF

UniProtKB: Pleiotropic regulator 1

Macromolecule #8: Pre-mRNA-processing factor 17

• Macromolecule: Name: Pre-mRNA-processing factor 17 / type: protein_or_peptide / ID: 8 / 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 #9: Pre-mRNA-splicing factor 38A

• Macromolecule: Name: Pre-mRNA-splicing factor 38A / type: protein_or_peptide / ID: 9 / 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 #10: Pre-mRNA-processing-splicing factor 8

• Macromolecule: Name: Pre-mRNA-processing-splicing factor 8 / type: protein_or_peptide / ID: 10 / 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 #11: Pre-mRNA-splicing factor RBM22

• Macromolecule: Name: Pre-mRNA-splicing factor RBM22 / type: protein_or_peptide / ID: 11 / 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 #12: SNW domain-containing protein 1

• Macromolecule: Name: SNW domain-containing protein 1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 61.610703 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 EHEHEGKKRR KE

UniProtKB: SNW domain-containing protein 1

Macromolecule #13: Zinc finger matrin-type protein 2

• Macromolecule: Name: Zinc finger matrin-type protein 2 / type: protein_or_peptide / ID: 13 / 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 #17: Ubiquitin-like protein 5

• Macromolecule: Name: Ubiquitin-like protein 5 / type: protein_or_peptide / ID: 17 / 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 #7: MINX M3 pre-mRNA

• Macromolecule: Name: MINX M3 pre-mRNA / type: rna / ID: 7 / Number of copies: 1
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 73.712359 KDa

Sequence

String:

GGGAGACGGA AUUCGAGCUC GCCCACUCUU GGAUCGGAAA CCCGUCGGCC UCCGAACGGU AAGAGCCUAG CAUGUAGAAC UGGUUACCU GCAGCCCAAG CUUGCUGCAC GUCUAGGGCG CAGUAGUCCA GGGUUUCCUU GAUGAUGUCA UACUUAUCCU G UCCCUUUU UUUUCCACAG CUCGCGGUUG AGGACAAACU CUUCGCGGUC UUUCCAGUGG GGAUCCAAUA UC

Macromolecule #14: U2 snRNA

• Macromolecule: Name: U2 snRNA / type: rna / ID: 14 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.186445 KDa

Sequence

String:

AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUGUAGUAUC UGUUCUUAUC AGUUUAAUAU CUGAUACGUC CUCUAUCCGA GGACAAUAU AUUAAAUGGA UUUUUGGAGC AGGGAGAUGG AAUAGGAGCU UGCUCCGUCC ACUCCACGCA UCGACCUGGU A UUGCAGUA CCUCCAGGAA CGGUGCACCC

GENBANK: GENBANK: X02665.1

Macromolecule #15: U5 snRNA

• Macromolecule: Name: U5 snRNA / type: rna / ID: 15 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 36.908668 KDa

Sequence

String:

AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAU UUUUUGAGCC UUGCCUUGGC AAGGCUA

GENBANK: GENBANK: X01691.1

Macromolecule #16: U6 snRNA

• Macromolecule: Name: U6 snRNA / type: rna / ID: 16 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 34.09827 KDa

Sequence

String:

GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGU GAAGCGUUCC AUAUUUU

Macromolecule #18: GUANOSINE-5'-TRIPHOSPHATE

• Macromolecule: Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 18 / Number of copies: 1 / Formula: GTP
• Molecular weight: Theoretical: 523.18 Da

Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

Macromolecule #19: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #20: D-chiro inositol hexakisphosphate

• Macromolecule: Name: D-chiro inositol hexakisphosphate / type: ligand / ID: 20 / Number of copies: 1 / Formula: KGN
• Molecular weight: Theoretical: 660.035 Da

Chemical component information

ChemComp-KGN:
D-chiro inositol hexakisphosphate

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.9
• Grid: Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
• Vitrification: Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 2.25 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
• 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: cryoSPARC ab initio reconstruction
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 39336
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: RIGID BODY FIT

Output model

PDB-7aav:
Human pre-Bact-2 spliceosome core structure