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- EMDB-49389: CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRAT... -

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Entry
Database: EMDB / ID: EMD-49389
TitleCRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA FOCUS MAP
Map dataCRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP)
Sample
  • Complex: HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 3
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 2
    • Protein or peptide: Symplekin
KeywordsMethylated RNA / 3' end processing / U7 snRNP / Histone pre-mRNA / RNA BINDING PROTEIN
Function / homology
Function and homology information


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 / nuclear stress granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing ...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 / nuclear stress granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of G1/S transition of mitotic cell cycle / bicellular tight junction / negative regulation of protein binding / RNA endonuclease activity / mRNA processing / cytoskeleton / cell adhesion / postsynapse / nuclear body / ribonucleoprotein complex / glutamatergic synapse / RNA binding / nucleoplasm / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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
Symplekin / Cleavage and polyadenylation specificity factor subunit 2 / Cleavage and polyadenylation specificity factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsDesotell A / Tong L
Funding support United States, 2 items
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 22, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49389.png

Downloads & links

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Map

FileDownload / File: emd_49389.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.39055774 - 0.665857
Average (Standard dev.)0.000024665565 (±0.0041593676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49389_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49389_half_map_2.map
AnnotationHalf Map 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 : HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA

EntireName: HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
Components
  • Complex: HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 3
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 2
    • Protein or peptide: Symplekin

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Supramolecule #1: HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA

SupramoleculeName: HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 485 KDa

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Macromolecule #1: Cleavage and polyadenylation specificity factor subunit 3

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 3
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.580883 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAIPAEESD QLLIRPLGAG QEVGRSCIIL EFKGRKIMLD CGIHPGLEGM DALPYIDLID PAEIDLLLIS HFHLDHCGAL PWFLQKTSF KGRTFMTHAT KAIYRWLLSD YVKVSNISAD DMLYTETDLE ESMDKIETIN FHEVKEVAGI KFWCYHAGHV L GAAMFMIE ...String:
MSAIPAEESD QLLIRPLGAG QEVGRSCIIL EFKGRKIMLD CGIHPGLEGM DALPYIDLID PAEIDLLLIS HFHLDHCGAL PWFLQKTSF KGRTFMTHAT KAIYRWLLSD YVKVSNISAD DMLYTETDLE ESMDKIETIN FHEVKEVAGI KFWCYHAGHV L GAAMFMIE IAGVKLLYTG DFSRQEDRHL MAAEIPNIKP DILIIESTYG THIHEKREER EARFCNTVHD IVNRGGRGLI PV FALGRAQ ELLLILDEYW QNHPELHDIP IYYASSLAKK CMAVYQTYVN AMNDKIRKQI NINNPFVFKH ISNLKSMDHF DDI GPSVVM ASPGMMQSGL SRELFESWCT DKRNGVIIAG YCVEGTLAKH IMSEPEEITT MSGQKLPLKM SVDYISFSAH TDYQ QTSEF IRALKPPHVI LVHGEQNEMA RLKAALIREY EDNDEVHIEV HNPRNTEAVT LNFRGEKLAK VMGFLADKKP EQGQR VSGI LVKRNFNYHI LSPCDLSNYT DLAMSTVKQT QAIPYTGPFN LLCYQLQKLT GDVEELEIQE KPALKVFKNI TVIQEP GMV VLEWLANPSN DMYADTVTTV ILEVQSNPKI RKGAVQKVSK KLEMHVYSKR LEIMLQDIFG EDCVSVKDDS ILSVTVD GK TANLNLETRT VECEEGSEDD ESLREMVELA AQRLYEALTP VH

UniProtKB: Cleavage and polyadenylation specificity factor subunit 3

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Macromolecule #2: Cleavage and polyadenylation specificity factor subunit 2

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.597734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTSIIKLTTL SGVQEESALC YLLQVDEFRF LLDCGWDEHF SMDIIDSLRK HVHQIDAVLL SHPDPLHLGA LPYAVGKLGL NCAIYATIP VYKMGQMFMY DLYQSRHNTE DFTLFTLDDV DAAFDKIQQL KFSQIVNLKG KGHGLSITPL PAGHMIGGTI W KIVKDGEE ...String:
MTSIIKLTTL SGVQEESALC YLLQVDEFRF LLDCGWDEHF SMDIIDSLRK HVHQIDAVLL SHPDPLHLGA LPYAVGKLGL NCAIYATIP VYKMGQMFMY DLYQSRHNTE DFTLFTLDDV DAAFDKIQQL KFSQIVNLKG KGHGLSITPL PAGHMIGGTI W KIVKDGEE EIVYAVDFNH KREIHLNGCS LEMLSRPSLL ITDSFNATYV QPRRKQRDEQ LLTNVLETLR GDGNVLIAVD TA GRVLELA QLLDQIWRTK DAGLGVYSLA LLNNVSYNVV EFSKSQVEWM SDKLMRCFED KRNNPFQFRH LSLCHGLSDL ARV PSPKVV LASQPDLECG FSRDLFIQWC QDPKNSIILT YRTTPGTLAR FLIDNPSEKI TEIELRKRVK LEGKELEEYL EKEK LKKEA AKKLEQSKEA DIDSSDESDI EEDIDQPSAH KTKHDLMMKG EGSRKGSFFK QAKKSYPMFP APEERIKWDE YGEII KPED FLVPELQATE EEKSKLESGL TNGDEPMDQD LSDVPTKCIS TTESIEIKAR VTYIDYEGRS DGDSIKKIIN QMKPRQ LII VHGPPEASQD LAECCRAFGG KDIKVYMPKL HETVDATSET HIYQVRLKDS LVSSLQFCKA KDAELAWIDG VLDMRVS KV DTGVILEEGE LKDDGEDSEM QVEAPSDSSV IAQQKAMKSL FGDDEKETGE ESEIIPTLEP LPPHEVPGHQ SVFMNEPR L SDFKQVLLRE GIQAEFVGGV LVCNNQVAVR RTETGRIGLE GCLCQDFYRI RDLLYEQYAI V

UniProtKB: Cleavage and polyadenylation specificity factor subunit 2

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Macromolecule #3: Symplekin

MacromoleculeName: Symplekin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.355125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTTSERVVDL LNQAALITND SKITVLKQVQ ELIINKDPTL LDNFLDEIIA FQADKSIEVR KFVIGFIEEA CKRDIELLLK LIANLNMLL RDENVNVVKK AILTMTQLYK VALQWMVKSR VISELQEACW DMVSAMAGDI ILLLDSDNDG IRTHAIKFVE G LIVTLSPR ...String:
MTTSERVVDL LNQAALITND SKITVLKQVQ ELIINKDPTL LDNFLDEIIA FQADKSIEVR KFVIGFIEEA CKRDIELLLK LIANLNMLL RDENVNVVKK AILTMTQLYK VALQWMVKSR VISELQEACW DMVSAMAGDI ILLLDSDNDG IRTHAIKFVE G LIVTLSPR MADSEIPRRQ EHDISLDRIP RDHPYIQYNV LWEEGKAALE QLLKFMVHPA ISSINLTTAL GSLANIARQR PM FMSEVIQ AYETLHANLP PTLAKSQVSS VRKNLKLHLL SVLKHPASLE FQAQITTLLV DLGTPQAEIA RNMPSSKDTR KRP RDDSDS TLKKMKLEPN LGEDDEDKDL EPGPSGTSKA SAQISGQSDT DITAEFLQPL LTPDNVANLV LISMVYLPEA MPAS FQAIY TPVESAGTEA QIKHLARLMA TQMTAAGLGP GVEQTKQCKE EPKEEKVVKT ESVLIKRRLS AQGQAISVVG SLSSM SPLE EEAPQAKRRP EPIIPVTQPR LAGAGGRKKI FRLSDVLKPL TDAQVEAMKL GAVKRILRAE KAVACSGAAQ VRIKIL ASL VTQFNSGLKA EVLSFILEDV RARLDLAFAW LYQEYNAYLA AGASGSLDKY EDCLIRLLSG LQEKPDQKDG IFTKVVL EA PLITESALEV VRKYCEDESR TYLGMSTLRD LIFKRPSRQF QYLHVLLDLS SHEKDKVRSQ ALLFIKRMYE KEQLREYV E KFALNYLQLL VHPNPPSVLF GADKDTEVAA PWTEETVKQC LYLYLALLPQ NHKLIHELAA VYTEAIADIK RTVLRVIEQ PIRGMGMNSP ELLLLVENCP KGAETLVTRC LHSLTDKVPP SPELVKRVRD LYHKRLPDVR FLIPVLNGLE KKEVIQALPK LIKLNPIVV KEVFNRLLGT QHGEGNSALS PLNPGELLIA LHNIDSVKCD MKSIIKATNL CFAERNVYTS EVLAVVMQQL M EQSPLPML LMRTVIQSLT MYPRLGGFVM NILSRLIMKQ VWKYPKVWEG FIKCCQRTKP QSFQVILQLP PQQLGAVFDK CP ELREPLL AHVRSFTPHQ QAHIPNSIMT ILEAS

UniProtKB: Symplekin

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClsodium chloride
10.0 mMEDTAEthylenediaminetetraacetic Acid
5.0 mMDTTDithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 14 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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: 8741039
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: AlphaFold prediction of the three proteins.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168875
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9ngo:
CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP)

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