[English] 日本語
Yorodumi
- PDB-9gcl: Structure of the U11 snRNP C-lobe -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gcl
TitleStructure of the U11 snRNP C-lobe
Components
  • (Small nuclear ribonucleoprotein ...) x 6
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • U11 snRNA
  • U11/U12 small nuclear ribonucleoprotein 48 kDa protein
  • Zinc finger matrin-type protein 5
KeywordsSPLICING / minor spliceosome / U11 snRNP / RNA-protein complex
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 RNA binding / telomerase holoenzyme complex / SMN-Sm protein complex / P granule / 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
: / RNA / RNA (> 10) / RNA (> 100) / 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 ...: / RNA / RNA (> 10) / RNA (> 100) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhao, J. / Galej, W.P.
Funding supportEuropean Union, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Zinc finger matrin-type protein 5
h: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D3
k: Small nuclear ribonucleoprotein-associated proteins B and B'
l: Small nuclear ribonucleoprotein E
m: Small nuclear ribonucleoprotein F
n: Small nuclear ribonucleoprotein G
F: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
i: Small nuclear ribonucleoprotein Sm D2
A: U11 snRNA


Theoretical massNumber of molelcules
Total (without water)198,04810
Polymers198,04810
Non-polymers00
Water00
1


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

-
Components

-
Protein , 3 types, 3 molecules EkF

#1: Protein Zinc finger matrin-type protein 5 / U11/U12 small nuclear ribonucleoprotein 20 kDa protein / U11/U12 snRNP 20 kDa protein / U11/U12-20K


Mass: 20002.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMAT5 / Production host: Homo sapiens (human) / References: UniProt: Q9UDW3
#4: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPB, COD, SNRPB1 / Production host: Homo sapiens (human) / References: UniProt: P14678
#8: Protein U11/U12 small nuclear ribonucleoprotein 48 kDa protein / U11/U12 snRNP 48 kDa protein / U11/U12-48K


Mass: 40042.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP48, C6orf151 / Production host: Homo sapiens (human) / References: UniProt: Q6IEG0

-
Small nuclear ribonucleoprotein ... , 6 types, 6 molecules hjlmni

#2: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Production host: Homo sapiens (human) / References: UniProt: P62314
#3: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD3 / Production host: Homo sapiens (human) / References: UniProt: P62318
#5: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Production host: Homo sapiens (human) / References: UniProt: P62304
#6: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Production host: Homo sapiens (human) / References: UniProt: P62306
#7: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Homo sapiens (human) / References: UniProt: P62308
#9: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2, SNRPD1 / Production host: Homo sapiens (human) / References: UniProt: P62316

-
RNA chain , 1 types, 1 molecules A

#10: RNA chain U11 snRNA


Mass: 43497.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: GenBank: 161169046

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Structure of the apo-U11 snRNP 3-lobe / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9 / Details: 20 mM HEPES-KOH, pH 7.9 200 mM KCl 2 mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMpotassium chlorideKCl1
22 mMmagnesium chlorideMgCl21
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Preliminary grid screening was performed on Glacios.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41.73 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 30164 / Details: Images were colleted in EER format
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.1particle selection
2SerialEMimage acquisition
7UCSF ChimeraX1.6.1model fitting
9cryoSPARCv4.3.1initial Euler assignment
10cryoSPARCv4.3.1final Euler assignment
11cryoSPARCv4.3.1classification
12cryoSPARCv4.3.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 7144222 / Details: Topaz picking is performed with user-trained model
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222666 / Symmetry type: POINT
Atomic model buildingB value: 71.2 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correction coefficient / Details: refinement is done in Phenix
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeInitial refinement model-IDSource nameTypePdb chain residue range
1AF-Q9UDW3-F1E1-1701AlphaFoldin silico model
2AF-Q6IEG0-F1F1-3392AlphaFoldin silico model
34PJO

4pjo

i4PJOi11-1143PDBexperimental model11-114
44PJO

4pjo

m4PJOm2-753PDBexperimental model2-75
54PJO

4pjo

l4PJOl14-903PDBexperimental model14-90
64PJO

4pjo

n4PJOn4-763PDBexperimental model4-76
74PJO

4pjo

j4PJOj3-833PDBexperimental model3-83
84PJO

4pjo

k4PJOk6-913PDBexperimental model6-91
94PJO

4pjo

h4PJOh2-823PDBexperimental model2-82
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 105.55 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037518
ELECTRON MICROSCOPYf_angle_d0.65910334
ELECTRON MICROSCOPYf_chiral_restr0.04151193
ELECTRON MICROSCOPYf_plane_restr0.00511160
ELECTRON MICROSCOPYf_dihedral_angle_d14.36661389

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more