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- PDB-9nh6: CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable ... -

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Entry
Database: PDB / ID: 9nh6
TitleCRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (COMPOSITE MAP)
Components
  • (Cleavage and polyadenylation specificity factor subunit ...) x 2
  • (Small nuclear ribonucleoprotein ...) x 4
  • (U7 snRNA-associated Sm-like protein ...) x 2
  • Cleavage stimulation factor subunit 3
  • Methylated H2A* pre-mRNA
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Symplekin
  • U7 snRNA
KeywordsRNA BINDING PROTEIN/RNA / Methylated RNA / 3' end processing / U7 snRNP / Histone pre-mRNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


cytoplasmic U snRNP body / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / 5'-3' RNA exonuclease activity / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / U2 snRNP binding / regulation of chromatin organization / U7 snRNA binding / histone pre-mRNA DCP binding ...cytoplasmic U snRNP body / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / 5'-3' RNA exonuclease activity / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / U2 snRNP binding / regulation of chromatin organization / U7 snRNA binding / histone pre-mRNA DCP binding / nuclear stress granule / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / methylosome / pICln-Sm protein complex / mRNA 3'-end processing / snRNP binding / Transport of Mature mRNA Derived from an Intronless Transcript / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA 3'-end processing / U2-type precatalytic spliceosome / P granule / telomerase holoenzyme complex / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U4 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle / bicellular tight junction / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / negative regulation of protein binding / catalytic step 2 spliceosome / RNA endonuclease activity / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / cytoskeleton / cell adhesion / postsynapse / nuclear body / ribonucleoprotein complex / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / : / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C ...Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / : / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Metallo-beta-lactamase superfamily domain / : / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / 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 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U7 snRNA-associated Sm-like protein LSm11 / Symplekin / U7 snRNA-associated Sm-like protein LSm10 ...RNA / RNA (> 10) / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U7 snRNA-associated Sm-like protein LSm11 / Symplekin / U7 snRNA-associated Sm-like protein LSm10 / Cleavage and polyadenylation specificity factor subunit 2 / Cleavage and polyadenylation specificity factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Trichoplusia ni (cabbage looper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsDesotell, A. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM029832 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: An N-terminal helix of Lsm11 stabilizes CPSF73 in U7 snRNP for histone pre-mRNA 3'-end processing.
Authors: Anthony Desotell / William F Marzluff / Zbigniew Dominski / Liang Tong /
Abstract: The U7 snRNP (small nuclear ribonucleoprotein) is responsible for the 3'-end processing of replication-dependent histone messenger RNA precursors (pre-mRNAs). A helix in the Lsm11 N-terminal ...The U7 snRNP (small nuclear ribonucleoprotein) is responsible for the 3'-end processing of replication-dependent histone messenger RNA precursors (pre-mRNAs). A helix in the Lsm11 N-terminal extension contacts the metallo-β-lactamase domain of the U7 snRNP endonuclease CPSF73. We mutated or deleted this helix and found that the mutant machineries had substantially reduced cleavage activity toward the pre-mRNA. Our cryo-electron microscopy (cryo-EM) studies indicated that the helix was important for helping to hold CPSF73 in its correct position for the cleavage reaction. We also reconstituted a wild-type U7 snRNP in complex with a methylated, noncleavable pre-mRNA. We observed that CPSF73 could achieve an open conformation independent of RNA binding to its active site. Finally, we found that a previously uninterpreted EM density for a small helix at the CPSF73-CPSF100 interface belonged to the C-terminal end of CstF77, copurified from insect cells and highly conserved among CstF77 homologs. This CstF77 binding site had a small effect on the cleavage activity of U7 snRNP. Overall, our studies have revealed the importance of the conserved helix in the Lsm11 N-terminal extension for U7 snRNP, provided structural evidence that CPSF73 can achieve an open, active conformation without RNA binding in its active site, and identified a previously unknown binding site for CstF77 in CPSF100.
History
DepositionFeb 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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
A: Small nuclear ribonucleoprotein Sm D3
B: Small nuclear ribonucleoprotein-associated proteins B and B'
F: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein E
G: Small nuclear ribonucleoprotein G
C: U7 snRNA-associated Sm-like protein LSm10
D: U7 snRNA-associated Sm-like protein LSm11
H: Cleavage and polyadenylation specificity factor subunit 3
I: Cleavage and polyadenylation specificity factor subunit 2
J: Symplekin
K: Cleavage stimulation factor subunit 3
Z: U7 snRNA
Y: Methylated H2A* pre-mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,21815
Polymers438,08813
Non-polymers1312
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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Small nuclear ribonucleoprotein ... , 4 types, 4 molecules AFEG

#1: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 16111.671 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P62318
#3: 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: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P62306
#4: 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: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P62304
#5: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 9579.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P62308

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Protein , 2 types, 2 molecules BJ

#2: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 10911.931 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: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P14678
#10: Protein Symplekin


Mass: 120355.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYMPK, SPK / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92797

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U7 snRNA-associated Sm-like protein ... , 2 types, 2 molecules CD

#6: Protein U7 snRNA-associated Sm-like protein LSm10


Mass: 14102.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSM10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q969L4
#7: Protein U7 snRNA-associated Sm-like protein LSm11


Mass: 40821.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSM11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P83369

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Cleavage and polyadenylation specificity factor subunit ... , 2 types, 2 molecules HI

#8: Protein Cleavage and polyadenylation specificity factor subunit 3 / Cleavage and polyadenylation specificity factor 73 kDa subunit / CPSF 73 kDa subunit / mRNA 3'-end- ...Cleavage and polyadenylation specificity factor 73 kDa subunit / CPSF 73 kDa subunit / mRNA 3'-end-processing endonuclease CPSF-73


Mass: 77580.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF3, CPSF73 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9UKF6, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#9: Protein Cleavage and polyadenylation specificity factor subunit 2 / Cleavage and polyadenylation specificity factor 100 kDa subunit / CPSF 100 kDa subunit


Mass: 88597.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF2, CPSF100, KIAA1367 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9P2I0

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RNA chain , 2 types, 2 molecules ZY

#12: RNA chain U7 snRNA


Mass: 20358.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#13: RNA chain Methylated H2A* pre-mRNA


Mass: 18022.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein/peptide / Non-polymers , 2 types, 3 molecules K

#11: Protein/peptide Cleavage stimulation factor subunit 3


Mass: 1094.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)
#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / 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: HUMAN U7 SNRNP ASSEMBLED WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
Type: COMPLEX / Entity ID: #1-#13 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2100 mMsodium chlorideNaCl1
310 mMEthylenediaminetetraacetic AcidEDTA1
45 mMDithiothreitolDTT1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv.4.4.1+240110particle selection
7UCSF ChimeraXmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8741039
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168875 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16v4X

6v4x

16v4X1PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 2.82 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419962
ELECTRON MICROSCOPYf_angle_d0.78627202
ELECTRON MICROSCOPYf_dihedral_angle_d11.3613222
ELECTRON MICROSCOPYf_chiral_restr0.053177
ELECTRON MICROSCOPYf_plane_restr0.0063260

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