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- PDB-9r3d: Cryo-EM structure of the human pre-Bact-OTS complex (whole map) -

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Basic information

Entry
Database: PDB / ID: 9r3d
TitleCryo-EM structure of the human pre-Bact-OTS complex (whole map)
Components
  • (Pre-mRNA-splicing factor ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Microfibrillar-associated protein 1
  • Pre-mRNA-processing factor 17
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • RING-type E3 ubiquitin-protein ligase PPIL2
  • SNW domain-containing protein 1
  • Transcription elongation regulator 1
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
  • U5 snRNA
  • U6 snRNA
  • Ubiquitin-like protein 5
  • WW domain-binding protein 11
  • Zinc finger matrin-type protein 2
  • pre-mRNA
KeywordsSPLICING / spliceosome
Function / homology
Function and homology information


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) / embryonic brain development / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pre-mRNA binding / positive regulation of mRNA splicing, via spliceosome ...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) / embryonic brain development / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pre-mRNA binding / positive regulation of mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / mRNA 3'-end processing / host-mediated activation of viral transcription / positive regulation of vitamin D receptor signaling pathway / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA polymerase binding / Notch binding / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / 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 / positive regulation of neurogenesis / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / ubiquitin-ubiquitin ligase activity / precatalytic spliceosome / Notch-HLH transcription pathway / WW domain binding / ubiquitin-like protein conjugating enzyme binding / Formation of paraxial mesoderm / 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 / U6 snRNA binding / U2 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 RNA splicing / positive regulation of protein export from nucleus / 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 / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / Golgi lumen / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / cellular response to xenobiotic stimulus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to tumor necrosis factor / mRNA processing / nuclear matrix / protein tag activity / protein polyubiquitination / calcium-dependent protein binding / rRNA processing / osteoblast differentiation / transcription corepressor activity / ubiquitin protein ligase activity / single-stranded DNA binding / sperm principal piece / protein folding / microtubule cytoskeleton / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / RNA helicase activity / nuclear speck / cilium
Similarity search - Function
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 ...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 / : / Modified RING finger domain / U-box domain / 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 / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Elongation factor G C-terminus / 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 / WW 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 / 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
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / 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 ...INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsZhang, Z. / Kumar, V. / Zhong, J. / Dybkov, O. / Kastner, B. / Urlaub, H. / Luhrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: 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
DepositionMay 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
5: U5 snRNA
6: U6 snRNA
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
C: 116 kDa U5 small nuclear ribonucleoprotein component
I: Pre-mRNA-splicing factor 38A
K: Microfibrillar-associated protein 1
Q: Protein BUD31 homolog
T: Transcription elongation regulator 1
X: WW domain-binding protein 11
Z: pre-mRNA
q: Ubiquitin-like protein 5
r: Zinc finger matrin-type protein 2
P7: Pre-mRNA-processing factor 17
A: Pre-mRNA-processing-splicing factor 8
P: Pre-mRNA-splicing factor RBM22
t: RING-type E3 ubiquitin-protein ligase PPIL2
S1: SNW domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,255,13218
Polymers1,254,47217
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 56Z

#1: RNA chain U5 snRNA


Mass: 24496.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain U6 snRNA


Mass: 27447.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#10: RNA chain pre-mRNA


Mass: 9307.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 12 types, 12 molecules BCKQTXqrP7AtS1

#3: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#4: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#6: Protein Microfibrillar-associated protein 1 / Spliceosome B complex protein MFAP1


Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55081
#7: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#8: Protein Transcription elongation regulator 1 / TATA box-binding protein-associated factor 2S / Transcription factor CA150


Mass: 124083.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14776
#9: Protein WW domain-binding protein 11 / WBP-11 / Npw38-binding protein / NpwBP / SH3 domain-binding protein SNP70 / Splicing factor that ...WBP-11 / Npw38-binding protein / NpwBP / SH3 domain-binding protein SNP70 / Splicing factor that interacts with PQBP-1 and PP1


Mass: 70098.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2W2
#11: Protein Ubiquitin-like protein 5


Mass: 8560.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZL1
#12: Protein Zinc finger matrin-type protein 2


Mass: 23664.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96NC0
#13: Protein Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#14: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#16: Protein RING-type E3 ubiquitin-protein ligase PPIL2 / CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive ...CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive peptidyl-prolyl cis-trans isomerase-like 2 / PPIase / Rotamase PPIL2


Mass: 58910.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13356, RING-type E3 ubiquitin transferase
#17: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 60326.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573

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Pre-mRNA-splicing factor ... , 2 types, 2 molecules IP

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


Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NAV1
#15: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64

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Non-polymers , 1 types, 1 molecules

#18: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: pre-Bact-OTS-complex / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.19.2_4158:model refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35015 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00243103
ELECTRON MICROSCOPYf_angle_d0.47159571
ELECTRON MICROSCOPYf_dihedral_angle_d10.0337820
ELECTRON MICROSCOPYf_chiral_restr0.0386890
ELECTRON MICROSCOPYf_plane_restr0.0037103

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