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- EMDB-51233: Structure of the U11 snRNP C-lobe -

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Basic information

Entry
Database: EMDB / ID: EMD-51233
TitleStructure of the U11 snRNP C-lobe
Map datamain map
Sample
  • Complex: Structure of the apo-U11 snRNP 3-lobe
    • Protein or peptide: Zinc finger matrin-type protein 5
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein-associated proteins B and B'
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D2
    • RNA: U11 snRNA
Keywordsminor spliceosome / U11 snRNP / RNA-protein complex / SPLICING
Function / homology
Function and homology information


U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation ...U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / telomerase holoenzyme complex / SMN-Sm protein complex / P granule / telomerase RNA binding / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / : / U11-48K-like CHHC zinc finger / Zinc finger CHHC U11-48K-type profile. / U1-C, C2H2-type zinc finger / U1 zinc finger / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Zinc finger, CCCH-type superfamily ...TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / : / U11-48K-like CHHC zinc finger / Zinc finger CHHC U11-48K-type profile. / U1-C, C2H2-type zinc finger / U1 zinc finger / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Zinc finger, CCCH-type superfamily / zinc finger / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Zinc finger C2H2 superfamily
Similarity search - Domain/homology
Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / U11/U12 small nuclear ribonucleoprotein 48 kDa protein / Zinc finger matrin-type protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhao J / Galej WP
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)950278European Union
CitationJournal: Mol Cell / Year: 2025
Title: Structural basis of 5' splice site recognition by the minor spliceosome.
Authors: Jiangfeng Zhao / Daniel Peter / Irina Brandina / Xiangyang Liu / Wojciech P Galej /
Abstract: The minor spliceosome catalyzes excision of U12-dependent introns from precursors of eukaryotic messenger RNAs (pre-mRNAs). This process is critical for many cellular functions, but the underlying ...The minor spliceosome catalyzes excision of U12-dependent introns from precursors of eukaryotic messenger RNAs (pre-mRNAs). This process is critical for many cellular functions, but the underlying molecular mechanisms remain elusive. Here, we report a cryoelectron microscopy (cryo-EM) reconstruction of the 13-subunit human U11 small nuclear ribonucleoprotein particle (snRNP) complex in apo and substrate-bound forms, revealing the architecture of the U11 small nuclear RNA (snRNA), five minor spliceosome-specific factors, and the mechanism of the U12-type 5' splice site (5'SS) recognition. SNRNP25 and SNRNP35 specifically recognize U11 snRNA, while PDCD7 bridges SNRNP25 and SNRNP48, located at the distal ends of the particle. SNRNP48 and ZMAT5 are positioned near the 5' end of U11 snRNA and stabilize binding of the incoming 5'SS. Recognition of the U12-type 5'SS is achieved through base-pairing to the 5' end of the U11 snRNA and unexpected, non-canonical base-triple interactions with the U11 snRNA stem-loop 3. Our structures provide mechanistic insights into U12-dependent intron recognition and the evolution of the splicing machinery.
History
DepositionAug 2, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51233.png

Downloads & links

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Map

FileDownload / File: emd_51233.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.22685733 - 0.40820327
Average (Standard dev.)-0.00001753118 (±0.006570928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 321.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_51233_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_51233_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the apo-U11 snRNP 3-lobe

EntireName: Structure of the apo-U11 snRNP 3-lobe
Components
  • Complex: Structure of the apo-U11 snRNP 3-lobe
    • Protein or peptide: Zinc finger matrin-type protein 5
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein-associated proteins B and B'
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D2
    • RNA: U11 snRNA

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Supramolecule #1: Structure of the apo-U11 snRNP 3-lobe

SupramoleculeName: Structure of the apo-U11 snRNP 3-lobe / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Zinc finger matrin-type protein 5

MacromoleculeName: Zinc finger matrin-type protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.002801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGKRYFCDYC DRSFQDNLHN RKKHLNGLQH LKAKKVWYDM FRDAAAILLD EQNKRPCRKF LLTGQCDFGS NCRFSHMSER DLQELSIQV EEERRAREWL LDAPELPEGH LEDWLEKRAK RLSSAPSSRA EPIRTTVFQY PVGWPPVQEL PPSLRAPPPG G WPLQPRVQ WG

UniProtKB: Zinc finger matrin-type protein 5

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Macromolecule #2: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.310653 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR EPVQLETLSI RGNNIRYFIL PDSLPLDTLL VDVEPKVKS KKREAVAGRG RGRGRGRGRG RGRGRGGPRR

UniProtKB: Small nuclear ribonucleoprotein Sm D1

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Macromolecule #3: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.940308 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ VYIRGSKIRF LILPDMLKNA PMLKSMKNK NQGSGAGRGK AAILKAQVAA RGRGRGMGRG NIFQKRR

UniProtKB: Small nuclear ribonucleoprotein Sm D3

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Macromolecule #4: Small nuclear ribonucleoprotein-associated proteins B and B'

MacromoleculeName: Small nuclear ribonucleoprotein-associated proteins B and B'
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.642131 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTVGKSSKML QHIDYRMRCI LQDGRIFIGT FKAFDKHMNL ILCDCDEFRK IKPKNSKQAE REEKRVLGLV LLRGENLVSM TVEGPPPKD TGIARVPLAG AAGGPGIGRA AGRGIPAGVP MPQAPAGLAG PVRGVGGPSQ QVMTPQGRGT VAAAAAAATA S IAGAPTQY ...String:
MTVGKSSKML QHIDYRMRCI LQDGRIFIGT FKAFDKHMNL ILCDCDEFRK IKPKNSKQAE REEKRVLGLV LLRGENLVSM TVEGPPPKD TGIARVPLAG AAGGPGIGRA AGRGIPAGVP MPQAPAGLAG PVRGVGGPSQ QVMTPQGRGT VAAAAAAATA S IAGAPTQY PPGRGGPPPP MGRGAPPPGM MGPPPGMRPP MGPPMGIPPG RGTPMGMPPP GMRPPPPGMR GPPPPGMRPP RP

UniProtKB: Small nuclear ribonucleoprotein-associated proteins B and B'

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Macromolecule #5: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.817601 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAYRGQGQKV QKVMVQPINL IFRYLQNRSR IQVWLYEQVN MRIEGCIIGF DEYMNLVLDD AEEIHSKTKS RKQLGRIMLK GDNITLLQS VSN

UniProtKB: Small nuclear ribonucleoprotein E

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Macromolecule #6: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.734171 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE

UniProtKB: Small nuclear ribonucleoprotein F

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Macromolecule #7: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.508084 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSKAHPPELK KFMDKKLSLK LNGGRHVQGI LRGFDPFMNL VIDECVEMAT SGQQNNIGMV VIRGNSIIML EALERV

UniProtKB: Small nuclear ribonucleoprotein G

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Macromolecule #8: U11/U12 small nuclear ribonucleoprotein 48 kDa protein

MacromoleculeName: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.042621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGEPPPVEE RRRLQEELNE FVESGCRTLE EVTASLGWDL DSLDPGEEEA AEDEVVICPY DSNHHMPKSS LAKHMASCRL RKMGYTKEE EDEMYNPEFF YENVKIPSIT LNKDSQFQII KQARTAVGKD SDCYNQRIYS SLPVEVPLNH KRFVCDLTQA D RLALYDFV ...String:
MEGEPPPVEE RRRLQEELNE FVESGCRTLE EVTASLGWDL DSLDPGEEEA AEDEVVICPY DSNHHMPKSS LAKHMASCRL RKMGYTKEE EDEMYNPEFF YENVKIPSIT LNKDSQFQII KQARTAVGKD SDCYNQRIYS SLPVEVPLNH KRFVCDLTQA D RLALYDFV VEETKKKRSD SQIIENDSDL FVDLAAKINQ DNSRKSPKSY LEILAEVRDY KRRRQSYRAK NVHITKKSYT EV IRDVINV HMEELSNHWQ EEQEKAEDDA EKNEERRSAS VDSRQSGGSY LDAECSRHRR DRSRSPHKRK RNKDKDKNCE SRR RKERDG ERHHSHKRRK QKI

UniProtKB: U11/U12 small nuclear ribonucleoprotein 48 kDa protein

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Macromolecule #9: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.551928 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSLLNKPKSE MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK KLLGRVKAFD RHCNMVLENV KEMWTEVPKS GKGKKKSKP VNKDRYISKM FLRGDSVIVV LRNPLIAGK

UniProtKB: Small nuclear ribonucleoprotein Sm D2

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Macromolecule #10: U11 snRNA

MacromoleculeName: U11 snRNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.497605 KDa
SequenceString:
AAAAAGGGCU UCUGUCGUGA GUGGCACACG UAGGGCAACU CGAUUGCUCU GCGUGCGGAA UCGACAUCAA GGGCUUUCGG AAGCAUAAU UUUUUGGUAU UUGGGCAGCU GGUGAUCGUU GGUCCCGGCG CCCUUU

GENBANK: GENBANK: NR_004407.1

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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

Concentration0.2 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
200.0 mMKClpotassium chloride
2.0 mMMgCl2magnesium chloride

Details: 20 mM HEPES-KOH, pH 7.9 200 mM KCl 2 mM MgCl2
GridModel: UltrAuFoil R2/2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed on Glacios.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 30164 / Average electron dose: 41.73 e/Å2 / Details: Images were colleted in EER format
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7144222 / Details: Topaz picking is performed with user-trained model
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.1) / Number images used: 222666
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. v4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 118000 / Software - Name: cryoSPARC (ver. v4.3.1)
Details: The heterogeneous refinement was performed to separate particles.

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Atomic model buiding 1

Initial model
PDB IDChain

3-f1

chain_id: E, residue_range: 1-170, source_name: AlphaFold, initial_model_type: in silico model

0-f1

chain_id: F, residue_range: 1-339, source_name: AlphaFold, initial_model_type: in silico model

4pjo

chain_id: i, residue_range: 11-114, source_name: PDB, initial_model_type: experimental model

4pjo

chain_id: m, residue_range: 2-75, source_name: PDB, initial_model_type: experimental model

4pjo

chain_id: l, residue_range: 14-90, source_name: PDB, initial_model_type: experimental model

4pjo

chain_id: n, residue_range: 4-76, source_name: PDB, initial_model_type: experimental model

4pjo

chain_id: j, residue_range: 3-83, source_name: PDB, initial_model_type: experimental model

4pjo

chain_id: k, residue_range: 6-91, source_name: PDB, initial_model_type: experimental model

4pjo

chain_id: h, residue_range: 2-82, source_name: PDB, initial_model_type: experimental model
Detailsrefinement is done in Phenix
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 71.2 / Target criteria: Cross-correction coefficient
Output model

PDB-9gcl:
Structure of the U11 snRNP C-lobe

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