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- EMDB-8013: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP -

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Basic information

Entry
Database: EMDB / ID: EMD-8013
TitleHead region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Map dataHead Region of yeast spliceosomal U4/U6.U5 tri-snRNP.
Sample
  • Complex: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
    • Protein or peptide: x 10 types
    • RNA: x 1 types
Function / homology
Function and homology information


maturation of 5S rRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome ...maturation of 5S rRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D3 ...SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D3 / Sec63 domain / Sec63 Brl domain / 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 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / Resolution: 4.2 Å
AuthorsNguyen THD / Galej WP / Bai XC / Oubridge C / Scheres SHW / Newman AJ / Nagai K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Nature / Year: 2015
Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
History
DepositionDec 15, 2015-
Header (metadata) releaseJan 27, 2016-
Map releaseJan 27, 2016-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
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  • Atomic models: PDB-5gao
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8013.png

Downloads & links

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Map

FileDownload / File: emd_8013.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHead Region of yeast spliceosomal U4/U6.U5 tri-snRNP.
Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07287737 - 0.15714578
Average (Standard dev.)-0.00023307164 (±0.003403494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 543.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z543.400543.400543.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0730.157-0.000

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Supplemental data

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Sample components

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Entire : Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP

EntireName: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Components
  • Complex: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
    • Protein or peptide: Small nuclear ribonucleoprotein-associated protein B
    • 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 E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: Snu66
    • Protein or peptide: Pre-mRNA-splicing helicase BRR2
    • RNA: Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence
    • Protein or peptide: Pre-mRNA-splicing factor 8

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Supramolecule #1: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP

SupramoleculeName: Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Small nuclear ribonucleoprotein-associated protein B

MacromoleculeName: Small nuclear ribonucleoprotein-associated protein B / type: protein_or_peptide / ID: 1
Details: The SmB protein from the U4 snRNP Sm protein ring. The C-terminus is disordered in this and other previously reported structures.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 22.42699 KDa
SequenceString: MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK LRPRKDSKDG TTLNIKVEKR VLGLTILRG EQILSTVVED KPLLSKKERL VRDKKEKKQA QKQTKLRKEK EKKPGKIAKP NTANAKHTSS NSREIAQPSS S RYNGGNDN ...String:
MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK LRPRKDSKDG TTLNIKVEKR VLGLTILRG EQILSTVVED KPLLSKKERL VRDKKEKKQA QKQTKLRKEK EKKPGKIAKP NTANAKHTSS NSREIAQPSS S RYNGGNDN IGANRSRFNN EAPPQTRKFQ PPPGFKRK

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Macromolecule #2: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 2
Details: The SmD1 protein from the U4 snRNP Sm protein ring.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 16.296798 KDa
SequenceString:
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP RLNKLNSNGI AMASLYLTGG QQPTASDNIA SLQYINIRG NTIRQIILPD SLNLDSLLVD QKQLNSLRRS GQIANDPSKK RRRDFGAPAN KRPRRGL

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Macromolecule #3: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 3
Details: The SmD2 protein from the U4 snRNP Sm protein ring.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 12.876066 KDa
SequenceString:
MSSQIIDRPK HELSRAELEE LEEFEFKHGP MSLINDAMVT RTPVIISLRN NHKIIARVKA FDRHCNMVLE NVKELWTEKK GKNVINRER FISKLFLRGD SVIVVLKTPV E

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Macromolecule #4: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 4
Details: The SmD3 protein from the U4 snRNP Sm protein ring.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 11.240139 KDa
SequenceString:
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSS RPMPPIRGPK RR

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Macromolecule #5: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 5 / Details: The SmE protein from the U4 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 10.385098 KDa
SequenceString:
MSNKVKTKAM VPPINCIFNF LQQQTPVTIW LFEQIGIRIK GKIVGFDEFM NVVIDEAVEI PVNSADGKED VEKGTPLGKI LLKGDNITL ITSAD

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Macromolecule #6: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 6 / Details: The SmF protein from the U4 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 9.669945 KDa
SequenceString:
MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV AGVSHGTLGE IFIRCNNVLY IRELPN

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Macromolecule #7: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 7 / Details: The SmG protein from the U4 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 8.490809 KDa
SequenceString:
MVSTPELKKY MDKKILLNIN GSRKVAGILR GYDIFLNVVL DDAMEINGED PANNHQLGLQ TVIRGNSIIS LEALDAI

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Macromolecule #8: Snu66

MacromoleculeName: Snu66 / type: protein_or_peptide / ID: 8
Details: NB: Snu66 protein has been mostly fitted as poly(Ala) into helices and extended polypeptide within the EM map. The authors do not believe the numbering to be accurate and it is likely incorrect.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 25.078721 KDa
SequenceString: AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA A AAAAAAAA ...String:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA A AAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AA AAAAAAA AAAAAAAAAA AAAAAAAAAA AARAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA TTK EAYKKL SQKFHGTKSN KK

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Macromolecule #9: Pre-mRNA-splicing helicase BRR2

MacromoleculeName: Pre-mRNA-splicing helicase BRR2 / type: protein_or_peptide / ID: 9
Details: Brr2 RNA helicase loaded onto U4 snRNA strand of the U4/U6 duplex between Stem 1 duplex and the 3' stem loop.
Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 246.470266 KDa
SequenceString: MTEHETKDKA KKIREIYRYD EMSNKVLKVD KRFMNTSQNP QRDAEISQPK SMSGRISAKD MGQGLCNNIN KGLKENDVAV EKTGKSASL KKIQQHNTIL NSSSDFRLHY YPKDPSNVET YEQILQWVTE VLGNDIPHDL IIGTADIFIR QLKENEENED G NIEERKEK ...String:
MTEHETKDKA KKIREIYRYD EMSNKVLKVD KRFMNTSQNP QRDAEISQPK SMSGRISAKD MGQGLCNNIN KGLKENDVAV EKTGKSASL KKIQQHNTIL NSSSDFRLHY YPKDPSNVET YEQILQWVTE VLGNDIPHDL IIGTADIFIR QLKENEENED G NIEERKEK IQHELGINID SLKFNELVKL MKNITDYETH PDNSNKQAVA ILADDEKSDE EEVTEMSNNA NVLGGEINDN ED DDEEYDY NDVEVNSKKK NKRALPNIEN DIIKLSDSKT SNIESVPIYS IDEFFLQRKL RSELGYKDTS VIQDLSEKIL NDI ETLEHN PVALEQKLVD LLKFENISLA EFILKNRSTI FWGIRLAKST ENEIPNLIEK MVAKGLNDLV EQYKFRETTH SKRE LDSGD DQPQSSEAKR TKFSNPAIPP VIDLEKIKFD ESSKLMTVTK VSLPEGSFKR VKPQYDEIHI PAPSKPVIDY ELKEI TSLP DWCQEAFPSS ETTSLNPIQS KVFHAAFEGD SNMLICAPTG SGKTNIALLT VLKALSHHYN PKTKKLNLSA FKIVYI APL KALVQEQVRE FQRRLAFLGI KVAELTGDSR LSRKQIDETQ VLVSTPEKWD ITTRNSNNLA IVELVRLLII DEIHLLH DD RGPVLESIVA RTFWASKYGQ EYPRIIGLSA TLPNYEDVGR FLRVPKEGLF YFDSSFRPCP LSQQFCGIKE RNSLKKLK A MNDACYEKVL ESINEGNQII VFVHSRKETS RTATWLKNKF AEENITHKLT KNDAGSKQIL KTEAANVLDP SLRKLIESG IGTHHAGLTR SDRSLSEDLF ADGLLQVLVC TATLAWGVNL PAHTVIIKGT DVYSPEKGSW EQLSPQDVLQ MLGRAGRPRY DTFGEGIII TDQSNVQYYL SVLNQQLPIE SQFVSKLVDN LNAEVVAGNI KCRNDAVNWL AYTYLYVRML ASPMLYKVPD I SSDGQLKK FRESLVHSAL CILKEQELVL YDAENDVIEA TDLGNIASSF YINHASMDVY NRELDEHTTQ IDLFRIFSMS EE FKYVSVR YEEKRELKQL LEKAPIPIRE DIDDPLAKVN VLLQSYFSQL KFEGFALNSD IVFIHQNAGR LLRAMFEICL KRG WGHPTR MLLNLCKSAT TKMWPTNCPL RQFKTCPVEV IKRLEASTVP WGDYLQLETP AEVGRAIRSE KYGKQVYDLL KRFP KMSVT CNAQPITRSV MRFNIEIIAD WIWDMNVHGS LEPFLLMLED TDGDSILYYD VLFITPDIVG HEFTLSFTYE LKQHN QNNL PPNFFLTLIS ENWWHSEFEI PVSFNGFKLP KKFPPPTPLL ENISISTSEL GNDDFSEVFE FKTFNKIQSQ VFESLY NSN DSVFVGSGKG TGKTAMAELA LLNHWRQNKG RAVYINPSGE KIDFLLSDWN KRFSHLAGGK IINKLGNDPS LNLKLLA KS HVLLATPVQF ELLSRRWRQR KNIQSLELMI YDDAHEISQG VYGAVYETLI SRMIFIATQL EKKIRFVCLS NCLANARD F GEWAGMTKSN IYNFSPSERI EPLEINIQSF KDVEHISFNF SMLQMAFEAS AAAAGNRNSS SVFLPSRKDC MEVASAFMK FSKAIEWDML NVEEEQIVPY IEKLTDGHLR APLKHGVGIL YKGMASNDER IVKRLYEYGA VSVLLISKDC SAFACKTDEV IILGTNLYD GAEHKYMPYT INELLEMVGL ASGNDSMAGK VLILTSHNMK AYYKKFLIEP LPTESYLQYI IHDTLNNEIA N SIIQSKQD CVDWFTYSYF YRRIHVNPSY YGVRDTSPHG ISVFLSNLVE TCLNDLVESS FIEIDDTEAE VTAEVNGGDD EA TEIISTL SNGLIASHYG VSFFTIQSFV SSLSNTSTLK NMLYVLSTAV EFESVPLRKG DRALLVKLSK RLPLRFPEHT SSG SVSFKV FLLLQAYFSR LELPVDFQND LKDILEKVVP LINVVVDILS ANGYLNATTA MDLAQMLIQG VWDVDNPLRQ IPHF NNKIL EKCKEINVET VYDIMALEDE ERDEILTLTD SQLAQVAAFV NNYPNVELTY SLNNSDSLIS GVKQKITIQL TRDVE PENL QVTSEKYPFD KLESWWLVLG EVSKKELYAI KKVTLNKETQ QYELEFDTPT SGKHNLTIWC VCDSYLDADK ELSFEI NVK

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Macromolecule #11: Pre-mRNA-splicing factor 8

MacromoleculeName: Pre-mRNA-splicing factor 8 / type: protein_or_peptide / ID: 11
Details: Prp8 Jab1/MPN domain is connected to the rest of the Prp8 protein by a flexible linker peptide.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 30.231008 KDa
SequenceString: SSKNEWRKSA IANTLLYLRL KNIYVSADDF VEEQNVYVLP KNLLKKFIEI SDVKIQVAAF IYGMSAKDHP KVKEIKTVVL VPQLGHVGS VQISNIPDIG DLPDTEGLEL LGWIHTQTEE LKFMAASEVA THSKLFADKK RDCIDISIFS TPGSVSLSAY N LTDEGYQW ...String:
SSKNEWRKSA IANTLLYLRL KNIYVSADDF VEEQNVYVLP KNLLKKFIEI SDVKIQVAAF IYGMSAKDHP KVKEIKTVVL VPQLGHVGS VQISNIPDIG DLPDTEGLEL LGWIHTQTEE LKFMAASEVA THSKLFADKK RDCIDISIFS TPGSVSLSAY N LTDEGYQW GEENKDIMNV LSEGFEPTFS THAQLLLSDR ITGNFIIPSG NVWNYTFMGT AFNQEGDYNF KYGIPLEFYN EM HRPVHFL QFSELAGDEE LEAEQIDVFS

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Macromolecule #10: Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence

MacromoleculeName: Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence
type: rna / ID: 10
Details: This U4 snRNA region has a disordered region between stem 1 of the U4/U6 snRNA duplex and where the RNA is loaded into Brr2 protein. The apical part of the 3' stem loop and the region ...Details: This U4 snRNA region has a disordered region between stem 1 of the U4/U6 snRNA duplex and where the RNA is loaded into Brr2 protein. The apical part of the 3' stem loop and the region following the Sm site are also disordered.
Number of copies: 1
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 30.615994 KDa
SequenceString:
GAAAUUUAAU UAUAAACCAG ACCGUCUCCU CAUGGUCAAU UCGGUGUUCG CUUUUGAAUA CUUCAAGACU AUGUAGGGAA UUUUUGGAA UACCUUU

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.9 / Component - Concentration: 1.0 mM / Component - Name: DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 6.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
Details: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number real images: 2477 / Average exposure time: 16.0 sec. / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 473827
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

2966


Details: Startup model was 60 Angstrom low-pass filtered.
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 140155
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4bgd

chain_id: B, residue_range: 442-2163

4bgd

chain_id: A, residue_range: 2143-2396
RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5gao:
Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP

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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

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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

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