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- EMDB-49402: CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49402
TitleCRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region)
Map dataSTRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
Sample
  • Complex: HUMAN U7 SNRNP ASSEMBLED WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
    • Protein or peptide: x 11 types
    • RNA: x 2 types
  • Ligand: x 1 types
KeywordsMethylated 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 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 24, 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_49402.png

Downloads & links

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Map

FileDownload / File: emd_49402.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
Projections & slices

Image control

Size
Brightness
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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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.4615054 - 0.6736607
Average (Standard dev.)0.00022738478 (±0.013659393)
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 B

Fileemd_49402_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49402_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HUMAN U7 SNRNP ASSEMBLED WITH METHYLATED H2A* SUBSTRATE PRE-MRNA

EntireName: HUMAN U7 SNRNP ASSEMBLED WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
Components
  • Complex: HUMAN U7 SNRNP ASSEMBLED WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
    • 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 F
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm10
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm11
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 3
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 2
    • Protein or peptide: Symplekin
    • Protein or peptide: Cleavage stimulation factor subunit 3
    • RNA: U7 snRNA
    • RNA: Methylated H2A* pre-mRNA
  • Ligand: ZINC ION

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

SupramoleculeName: HUMAN U7 SNRNP ASSEMBLED WITH METHYLATED H2A* SUBSTRATE PRE-MRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.111671 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ VYIRGSKIR FLILPDMLKN APMLKSMKNK NQGSGAGRGK AAILKAQVAA RGRGRGMGRG NIFQKRR

UniProtKB: Small nuclear ribonucleoprotein Sm D3

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Macromolecule #2: Small nuclear ribonucleoprotein-associated proteins B and B'

MacromoleculeName: Small nuclear ribonucleoprotein-associated proteins B and B'
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.911931 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTVGKSSKML QHIDYRMRCI LQDGRIFIGT FKAFDKHMNL ILCDCDEFRK IKPKNSKQAE REEKRVLGLV LLRGENLVSM TVEGPPPKD TGIARV

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

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Macromolecule #3: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.734171 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE

UniProtKB: Small nuclear ribonucleoprotein F

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Macromolecule #4: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.817601 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAYRGQGQKV QKVMVQPINL IFRYLQNRSR IQVWLYEQVN MRIEGCIIGF DEYMNLVLDD AEEIHSKTKS RKQLGRIMLK GDNITLLQS VSN

UniProtKB: Small nuclear ribonucleoprotein E

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Macromolecule #5: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.579236 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSKAHPPELK KFMDKKLSLK LNGGRHVQGI LRGFDPFMNL VIDECVEMAT SGQQNNIGMV VIRGNSIIML EALERVLEHH HHHH

UniProtKB: Small nuclear ribonucleoprotein G

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

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm10 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.102057 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAVSHSVKER TISENSLIIL LQGLQGRVTT VDLRDESVAH GRIDNVDAFM NIRLAKVTYT DRWGHQVKLD DLFVTGRNVR YVHIPDDVN ITSTIEQQLQ IIHRVRNFGG KGQGRWEFPP KNCK

UniProtKB: U7 snRNA-associated Sm-like protein LSm10

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Macromolecule #7: U7 snRNA-associated Sm-like protein LSm11

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm11 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.821117 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHSGG SMEERERGAR SAGAGSPARP PSPRLDVSSD SFDPLLALYA PRLPPIPYPN APCFNNVAEY ESFLRTGVRG GGRGRGRAR GAAAGSGVPA APGPSGRTRR RPDAPAPDPE RIQRLRRLMV AKEEGDGAAG AGRRGPGRSR KAPRNVLTRM P LHEGSPLG ...String:
MHHHHHHSGG SMEERERGAR SAGAGSPARP PSPRLDVSSD SFDPLLALYA PRLPPIPYPN APCFNNVAEY ESFLRTGVRG GGRGRGRAR GAAAGSGVPA APGPSGRTRR RPDAPAPDPE RIQRLRRLMV AKEEGDGAAG AGRRGPGRSR KAPRNVLTRM P LHEGSPLG ELHRCIREGV KVNVHIRTFK GLRGVCTGFL VAFDKFWNMA LTDVDETYRK PVLGKAYERD SSLTLTRLFD RL KLQDSSK KEADSKSAVE DSTLSRYSQT STWKLASVWG RADTGRGSHK RSRSVPSSLQ ASAREESRSE LSGRTTRTDG SSV GGTFSR ATTLSRGQSR KKKRKPKVDY QQVFTRHINQ IFIRGENVLL VHLAQ

UniProtKB: U7 snRNA-associated Sm-like protein LSm11

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Macromolecule #8: Cleavage and polyadenylation specificity factor subunit 3

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 3
type: protein_or_peptide / ID: 8 / 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 #9: Cleavage and polyadenylation specificity factor subunit 2

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 2
type: protein_or_peptide / ID: 9 / 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 #10: Symplekin

MacromoleculeName: Symplekin / type: protein_or_peptide / ID: 10 / 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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Macromolecule #11: Cleavage stimulation factor subunit 3

MacromoleculeName: Cleavage stimulation factor subunit 3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 1.094183 KDa
SequenceString:
NDIYRQRQ

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Macromolecule #12: U7 snRNA

MacromoleculeName: U7 snRNA / type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.358916 KDa
SequenceString:
GCAGUGUUAC AGCUCUUUUA GAAUUUGUCU AGUAGGCUUU CUGGCUUUUU ACCGGAAAGC CCCU

GENBANK: GENBANK: U47924.1

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Macromolecule #13: Methylated H2A* pre-mRNA

MacromoleculeName: Methylated H2A* pre-mRNA / type: rna / ID: 13 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.022895 KDa
SequenceString:
CCAAAGGCUC UUUUCAGAGC CAC(OMC)(OMC)(A2M)(OMC)(OMU)GA AUCAGAUAAA GAGCUGUAAC ACGGUA

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: PDB ENTRY
PDB model - PDB ID:

6v4x

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 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 modelPDB ID:

6v4x


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9nh5:
CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region)

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