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- EMDB-18984: Overall structure of the U11 snRNP -

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Basic information

Entry
Database: EMDB / ID: EMD-18984
TitleOverall structure of the U11 snRNP
Map data
Sample
  • Complex: Overall structure of the apo-U11 snRNP
    • RNA: x 1 types
    • Protein or peptide: x 12 types
Keywordsminor spliceosome / U11 snRNP / RNA-protein complex / SPLICING
Function / homology
Function and homology information


snRNA binding / 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 ...snRNA binding / 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 / methylosome / U1 snRNP binding / 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 / RNA Polymerase II Transcription Termination / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / intercellular bridge / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / response to glucocorticoid / 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 / mRNA binding / apoptotic process / nucleolus / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 7 / snRNP35, RNA recognition motif / : / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25kDa protein / SNRNP25, ubiquitin-like domain / Ubiquitin-like domain / TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / : / U11-48K-like CHHC zinc finger ...Programmed cell death protein 7 / snRNP35, RNA recognition motif / : / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25kDa protein / SNRNP25, ubiquitin-like domain / Ubiquitin-like domain / 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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Zinc finger C2H2 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Nucleotide-binding alpha-beta plait domain 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 35 kDa protein / U11/U12 small nuclear ribonucleoprotein 48 kDa protein / Programmed cell death protein 7 ...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 35 kDa protein / U11/U12 small nuclear ribonucleoprotein 48 kDa protein / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25 kDa protein / Zinc finger matrin-type protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionNov 26, 2023-
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_18984.png

Downloads & links

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Map

FileDownload / File: emd_18984.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.035
Minimum - Maximum-0.15026908 - 0.30080557
Average (Standard dev.)-0.000023941884 (±0.005693304)
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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Additional map: local filtered map

Fileemd_18984_additional_1.map
Annotationlocal filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map

Fileemd_18984_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map

Fileemd_18984_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Overall structure of the apo-U11 snRNP

EntireName: Overall structure of the apo-U11 snRNP
Components
  • Complex: Overall structure of the apo-U11 snRNP
    • RNA: U11 snRNA
    • Protein or peptide: U11/U12 small nuclear ribonucleoprotein 25 kDa protein
    • Protein or peptide: U11/U12 small nuclear ribonucleoprotein 35 kDa protein
    • Protein or peptide: Programmed cell death protein 7
    • Protein or peptide: Zinc finger matrin-type protein 5
    • Protein or peptide: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D2
    • 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

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Supramolecule #1: Overall structure of the apo-U11 snRNP

SupramoleculeName: Overall structure of the apo-U11 snRNP / 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: U11 snRNA

MacromoleculeName: U11 snRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.505629 KDa
SequenceString:
AAAAAGGGCU UCUGUCGUGA GUGGCACACG UAGGGCAACU CGAUUGCUCU GCGUGCGGAA UCGACAUCAA GAGAUUUCGG AAGCAUAAU UUUUUGGUAU UUGGGCAGCU GGUGAUCGUU GGUCCCGGCG CCCUUU

GENBANK: GENBANK: NR_004407.1

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Macromolecule #2: U11/U12 small nuclear ribonucleoprotein 25 kDa protein

MacromoleculeName: U11/U12 small nuclear ribonucleoprotein 25 kDa protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.290729 KDa
SequenceString:
MDVFQEGLAM VVQDPLLCDL PIQVTLEEVN SQIALEYGQA MTVRVCKMDG EVMPVVVVQS ATVLDLKKAI QRYVQLKQER EGGIQHISW SYVWRTYHLT SAGEKLTEDR KKLRDYGIRN RDEVSFIKKL RQK

UniProtKB: U11/U12 small nuclear ribonucleoprotein 25 kDa protein

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Macromolecule #3: U11/U12 small nuclear ribonucleoprotein 35 kDa protein

MacromoleculeName: U11/U12 small nuclear ribonucleoprotein 35 kDa protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.514471 KDa
SequenceString: MNDWMPIAKE YDPLKAGSID GTDEDPHDRA VWRAMLARYV PNKGVIGDPL LTLFVARLNL QTKEDKLKEV FSRYGDIRRL RLVRDLVTG FSKGYAFIEY KEERAVIKAY RDADGLVIDQ HEIFVDYELE RTLKGWIPRR LGGGLGGKKE SGQLRFGGRD R PFRKPINL ...String:
MNDWMPIAKE YDPLKAGSID GTDEDPHDRA VWRAMLARYV PNKGVIGDPL LTLFVARLNL QTKEDKLKEV FSRYGDIRRL RLVRDLVTG FSKGYAFIEY KEERAVIKAY RDADGLVIDQ HEIFVDYELE RTLKGWIPRR LGGGLGGKKE SGQLRFGGRD R PFRKPINL PVVKNDLYRE GKRERRERSR SRERHWDSRT RDRDHDRGRE KRWQEREPTR VWPDNDWERE RDFRDDRIKG RE KKERGK

UniProtKB: U11/U12 small nuclear ribonucleoprotein 35 kDa protein

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Macromolecule #4: Programmed cell death protein 7

MacromoleculeName: Programmed cell death protein 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.791984 KDa
SequenceString: MALPPFFGQG RPGPPPPQPP PPAPFGCPPP PLPSPAFPPP LPQRPGPFPG ASAPFLQPPL ALQPRASAEA SRGGGGAGAF YPVPPPPLP PPPPQCRPFP GTDAGERPRP PPPGPGPPWS PRWPEAPPPP ADVLGDAALQ RLRDRQWLEA VFGTPRRAGC P VPQRTHAG ...String:
MALPPFFGQG RPGPPPPQPP PPAPFGCPPP PLPSPAFPPP LPQRPGPFPG ASAPFLQPPL ALQPRASAEA SRGGGGAGAF YPVPPPPLP PPPPQCRPFP GTDAGERPRP PPPGPGPPWS PRWPEAPPPP ADVLGDAALQ RLRDRQWLEA VFGTPRRAGC P VPQRTHAG PSLGEVRARL LRALRLVRRL RGLSQALREA EADGAAWVLL YSQTAPLRAE LAERLQPLTQ AAYVGEARRR LE RVRRRRL RLRERARERE AEREAEAARA VEREQEIDRW RVKCVQEVEE KKREQELKAA ADGVLSEVRK KQADTKRMVD ILR ALEKLR KLRKEAAARK GVCPPASADE TFTHHLQRLR KLIKKRSELY EAEERALRVM LEGEQEEERK RELEKKQRKE KEKI LLQKR EIESKLFGDP DEFPLAHLLE PFRQYYLQAE HSLPALIQIR HDWDQYLVPS DHPKGNFVPQ GWVLPPLPSN DIWAT AVKL H

UniProtKB: Programmed cell death protein 7

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Macromolecule #5: Zinc finger matrin-type protein 5

MacromoleculeName: Zinc finger matrin-type protein 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.002801 KDa
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 #6: U11/U12 small nuclear ribonucleoprotein 48 kDa protein

MacromoleculeName: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.042621 KDa
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 #7: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.310653 KDa
SequenceString:
MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR EPVQLETLSI RGNNIRYFIL PDSLPLDTLL VDVEPKVKS KKREAVAGRG RGRGRGRGRG RGRGRGGPRR

UniProtKB: Small nuclear ribonucleoprotein Sm D1

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Macromolecule #8: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.551928 KDa
SequenceString:
MSLLNKPKSE MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK KLLGRVKAFD RHCNMVLENV KEMWTEVPKS GKGKKKSKP VNKDRYISKM FLRGDSVIVV LRNPLIAGK

UniProtKB: Small nuclear ribonucleoprotein Sm D2

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Macromolecule #9: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.940308 KDa
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 #10: Small nuclear ribonucleoprotein-associated proteins B and B'

MacromoleculeName: Small nuclear ribonucleoprotein-associated proteins B and B'
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.642131 KDa
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 #11: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.817601 KDa
SequenceString:
MAYRGQGQKV QKVMVQPINL IFRYLQNRSR IQVWLYEQVN MRIEGCIIGF DEYMNLVLDD AEEIHSKTKS RKQLGRIMLK GDNITLLQS VSN

UniProtKB: Small nuclear ribonucleoprotein E

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Macromolecule #12: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.734171 KDa
SequenceString:
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE

UniProtKB: Small nuclear ribonucleoprotein F

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Macromolecule #13: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.508084 KDa
SequenceString:
MSKAHPPELK KFMDKKLSLK LNGGRHVQGI LRGFDPFMNL VIDECVEMAT SGQQNNIGMV VIRGNSIIML EALERV

UniProtKB: Small nuclear ribonucleoprotein G

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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 / Material: GOLD / Mesh: 200 / 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 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

0-f1

chain_id: B, residue_range: 1-132, source_name: AlphaFold, initial_model_type: in silico model

0-f1

chain_id: C, residue_range: 1-246, source_name: AlphaFold, initial_model_type: in silico model

1-f1

chain_id: D, residue_range: 1-485, source_name: AlphaFold, initial_model_type: in silico model

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-8r7n:
Overall structure of the U11 snRNP

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  • 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

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