EMDB-18267: Structure of the human 20S U5 snRNP core

Basic information

Entry

Database: EMDB / ID: EMD-18267

• Title: Structure of the human 20S U5 snRNP core
• Map data: 20S U5 snRNP map

Sample

• Complex: 20S U5 snRNP complex purified from HEK293F cell line
  • Protein or peptide: x 13 types
  • RNA: x 1 types
• Ligand: x 1 types

• Keywords: snRNP / CD2BP2 / spliceosome / U5 / SPLICING

Function / homology

Function:

R-loop processing / RNA localization / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / Cajal body / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / ribonucleoprotein complex binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / cellular response to lipopolysaccharide / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / chromatin / GTP binding / nucleolus / enzyme binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm

Domain/homology:

CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Pre-mRNA-splicing factor Syf1-like / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Snu114, GTP-binding domain / Tetratricopeptide repeat / Sec63 Brl domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / 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 / Tetratricopeptide repeat / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / DEAD-box subfamily ATP-dependent helicases signature. / Sm domain profile. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / Elongation Factor G, domain II / Elongation Factor G, domain III / DEAD-box RNA helicase Q motif profile. / Translation elongation factor EFG/EF2, domain IV / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Elongation factor G, domain IV / Elongation factor G, domain IV / LSM domain superfamily / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / 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 / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Tetratricopeptide repeats / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / C2 domain superfamily / Tetratricopeptide repeat / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein 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 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily

Component:

U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / CD2 antigen cytoplasmic tail-binding protein 2 / 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 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Probable ATP-dependent RNA helicase DDX23

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.1 Å
• Authors: Schneider S / Galej WP

Funding support

European Union, 1 items

Organization	Grant number	Country
European Research Council (ERC)	950278	European Union

• Citation: Journal: Nat Struct Mol Biol / Year: 2024; Title: Structure of the human 20S U5 snRNP.; Authors: Sarah Schneider / Irina Brandina / Daniel Peter / Sonal Lagad / Angelique Fraudeau / Júlia Portell-Montserrat / Jonas Tholen / Jiangfeng Zhao / Wojciech P Galej / ; Abstract: The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process.

History

Deposition	Aug 19, 2023	-
Header (metadata) release	Mar 27, 2024	-
Map release	Mar 27, 2024	-
Update	Mar 27, 2024	-
Current status	Mar 27, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_18267.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: 20S U5 snRNP map
• Voxel size: X=Y=Z: 1.0449 Å

Density

Contour Level	By AUTHOR: 0.12
Minimum - Maximum	-0.39151424 - 1.0512583
Average (Standard dev.)	-0.000043258195 (±0.015958974)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 504 504 504 Spacing 504 504 504
Cell	A=B=C: 526.6296 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_18267_msk_1.map

Additional map: local resolution filtered map

• File: emd_18267_additional_1.map
• Annotation: local resolution filtered map

Additional map: sharpened map

• File: emd_18267_additional_2.map
• Annotation: sharpened map

Half map: half-map B

• File: emd_18267_half_map_1.map
• Annotation: half-map B

Half map: half-map A

• File: emd_18267_half_map_2.map
• Annotation: half-map A

Sample components

Entire : 20S U5 snRNP complex purified from HEK293F cell line

• Entire: Name: 20S U5 snRNP complex purified from HEK293F cell line

Components

• Complex: 20S U5 snRNP complex purified from HEK293F cell line
  • Protein or peptide: CD2 antigen cytoplasmic tail-binding protein 2
  • Protein or peptide: Pre-mRNA-processing-splicing factor 8
  • RNA: U5 snRNAU5 spliceosomal RNA
  • Protein or peptide: Pre-mRNA-processing factor 6
  • Protein or peptide: Probable ATP-dependent RNA helicase DDX23
  • Protein or peptide: 116 kDa U5 small nuclear ribonucleoprotein component
  • Protein or peptide: U5 small nuclear ribonucleoprotein 200 kDa helicase
  • Protein or peptide: Small nuclear ribonucleoprotein F
  • Protein or peptide: Small nuclear ribonucleoprotein G
  • 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
• Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate

Supramolecule #1: 20S U5 snRNP complex purified from HEK293F cell line

• Supramolecule: Name: 20S U5 snRNP complex purified from HEK293F cell line / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 1 MDa

Macromolecule #1: CD2 antigen cytoplasmic tail-binding protein 2

• Macromolecule: Name: CD2 antigen cytoplasmic tail-binding protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 37.687355 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MPKRKVTFQG VGDEEDEDEI IVPKKKLVDP VAGSGGPGSR FKGKHSLDSD EEEDDDDGGS SKYDILASED VEGQEAATLP SEGGVRITP FNLQEEMEEG HFDADGNYFL NRDAQIRDSW LDNIDWVKIR ERPPGQRQAS DSEEEDSLGQ TSMSAQALLE G LLELLLPR ETVAGALRRL GARGGGKGRK GPGQPSSPQR LDRLSGLADQ MVARGNLGVY QETRERLAMR LKGLGCQTLG PH NPTPPPS LDMFAEELAE EELETPTPTQ RGEAESRGDG LVDVMWEYKW ENTGDAELYG PFTSAQMQTW VSEGYFPDGV YCR KLDPPG GQFYNSKRID FDLYT

UniProtKB: CD2 antigen cytoplasmic tail-binding protein 2

Macromolecule #2: Pre-mRNA-processing-splicing factor 8

• Macromolecule: Name: Pre-mRNA-processing-splicing factor 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 273.97425 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MAGVFPYRGP GNPVPGPLAP LPDYMSEEKL QEKARKWQQL QAKRYAEKRK FGFVDAQKED MPPEHVRKII RDHGDMTNRK FRHDKRVYL GALKYMPHAV LKLLENMPMP WEQIRDVPVL YHITGAISFV NEIPWVIEPV YISQWGSMWI MMRREKRDRR H FKRMRFPP FDDEEPPLDY ADNILDVEPL EAIQLELDPE EDAPVLDWFY DHQPLRDSRK YVNGSTYQRW QFTLPMMSTL YR LANQLLT DLVDDNYFYL FDLKAFFTSK ALNMAIPGGP KFEPLVRDIN LQDEDWNEFN DINKIIIRQP IRTEYKIAFP YLY NNLPHH VHLTWYHTPN VVFIKTEDPD LPAFYFDPLI NPISHRHSVK SQEPLPDDDE EFELPEFVEP FLKDTPLYTD NTAN GIALL WAPRPFNLRS GRTRRALDIP LVKNWYREHC PAGQPVKVRV SYQKLLKYYV LNALKHRPPK AQKKRYLFRS FKATK FFQS TKLDWVEVGL QVCRQGYNML NLLIHRKNLN YLHLDYNFNL KPVKTLTTKE RKKSRFGNAF HLCREVLRLT KLVVDS HVQ YRLGNVDAFQ LADGLQYIFA HVGQLTGMYR YKYKLMRQIR MCKDLKHLIY YRFNTGPVGK GPGCGFWAAG WRVWLFF MR GITPLLERWL GNLLARQFEG RHSKGVAKTV TKQRVESHFD LELRAAVMHD ILDMMPEGIK QNKARTILQH LSEAWRCW K ANIPWKVPGL PTPIENMILR YVKAKADWWT NTAHYNRERI RRGATVDKTV CKKNLGRLTR LYLKAEQERQ HNYLKDGPY ITAEEAVAVY TTTVHWLESR RFSPIPFPPL SYKHDTKLLI LALERLKEAY SVKSRLNQSQ REELGLIEQA YDNPHEALSR IKRHLLTQR AFKEVGIEFM DLYSHLVPVY DVEPLEKITD AYLDQYLWYE ADKRRLFPPW IKPADTEPPP LLVYKWCQGI N NLQDVWET SEGECNVMLE SRFEKMYEKI DLTLLNRLLR LIVDHNIADY MTAKNNVVIN YKDMNHTNSY GIIRGLQFAS FI VQYYGLV MDLLVLGLHR ASEMAGPPQM PNDFLSFQDI ATEAAHPIRL FCRYIDRIHI FFRFTADEAR DLIQRYLTEH PDP NNENIV GYNNKKCWPR DARMRLMKHD VNLGRAVFWD IKNRLPRSVT TVQWENSFVS VYSKDNPNLL FNMCGFECRI LPKC RTSYE EFTHKDGVWN LQNEVTKERT AQCFLRVDDE SMQRFHNRVR QILMASGSTT FTKIVNKWNT ALIGLMTYFR EAVVN TQEL LDLLVKCENK IQTRIKIGLN SKMPSRFPPV VFYTPKELGG LGMLSMGHVL IPQSDLRWSK QTDVGITHFR SGMSHE EDQ LIPNLYRYIQ PWESEFIDSQ RVWAEYALKR QEAIAQNRRL TLEDLEDSWD RGIPRINTLF QKDRHTLAYD KGWRVRT DF KQYQVLKQNP FWWTHQRHDG KLWNLNNYRT DMIQALGGVE GILEHTLFKG TYFPTWEGLF WEKASGFEES MKWKKLTN A QRSGLNQIPN RRFTLWWSPT INRANVYVGF QVQLDLTGIF MHGKIPTLKI SLIQIFRAHL WQKIHESIVM DLCQVFDQE LDALEIETVQ KETIHPRKSY KMNSSCADIL LFASYKWNVS RPSLLADSKD VMDSTTTQKY WIDIQLRWGD YDSHDIERYA RAKFLDYTT DNMSIYPSPT GVLIAIDLAY NLHSAYGNWF PGSKPLIQQA MAKIMKANPA LYVLRERIRK GLQLYSSEPT E PYLSSQNY GELFSNQIIW FVDDTNVYRV TIHKTFEGNL TTKPINGAIF IFNPRTGQLF LKIIHTSVWA GQKRLGQLAK WK TAEEVAA LIRSLPVEEQ PKQIIVTRKG MLDPLEVHLL DFPNIVIKGS ELQLPFQACL KVEKFGDLIL KATEPQMVLF NLY DDWLKT ISSYTAFSRL ILILRALHVN NDRAKVILKP DKTTITEPHH IWPTLTDEEW IKVEVQLKDL ILADYGKKNN VNVA SLTQS EIRDIILGME ISAPSQQRQQ IAEIEKQTKE QSQLTATQTR TVNKHGDEII TSTTSNYETQ TFSSKTEWRV RAISA ANLH LRTNHIYVSS DDIKETGYTY ILPKNVLKKF ICISDLRAQI AGYLYGVSPP DNPQVKEIRC IVMVPQWGTH QTVHLP GQL PQHEYLKEME PLGWIHTQPN ESPQLSPQDV TTHAKIMADN PSWDGEKTII ITCSFTPGSC TLTAYKLTPS GYEWGRQ NT DKGNNPKGYL PSHYERVQML LSDRFLGFFM VPAQSSWNYN FMGVRHDPNM KYELQLANPK EFYHEVHRPS HFLNFALL Q EGEVYSADRE DLYA

UniProtKB: Pre-mRNA-processing-splicing factor 8

Macromolecule #4: Pre-mRNA-processing factor 6

• Macromolecule: Name: Pre-mRNA-processing factor 6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 107.092242 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MNKKKKPFLG MPAPLGYVPG LGRGATGFTT RSDIGPARDA NDPVDDRHAP PGKRTVGDQM KKNQAADDDD EDLNDTNYDE FNGYAGSLF SSGPYEKDDE EADAIYAALD KRMDERRKER REQREKEEIE KYRMERPKIQ QQFSDLKRKL AEVTEEEWLS I PEVGDARN KRQRNPRYEK LTPVPDSFFA KHLQTGENHT SVDPRQTQFG GLNTPYPGGL NTPYPGGMTP GLMTPGTGEL DM RKIGQAR NTLMDMRLSQ VSDSVSGQTV VDPKGYLTDL NSMIPTHGGD INDIKKARLL LKSVRETNPH HPPAWIASAR LEE VTGKLQ VARNLIMKGT EMCPKSEDVW LEAARLQPGD TAKAVVAQAV RHLPQSVRIY IRAAELETDI RAKKRVLRKA LEHV PNSVR LWKAAVELEE PEDARIMLSR AVECCPTSVE LWLALARLET YENARKVLNK ARENIPTDRH IWITAAKLEE ANGNT QMVE KIIDRAITSL RANGVEINRE QWIQDAEECD RAGSVATCQA VMRAVIGIGI EEEDRKHTWM EDADSCVAHN ALECAR AIY AYALQVFPSK KSVWLRAAYF EKNHGTRESL EALLQRAVAH CPKAEVLWLM GAKSKWLAGD VPAARSILAL AFQANPN SE EIWLAAVKLE SENDEYERAR RLLAKARSSA PTARVFMKSV KLEWVQDNIR AAQDLCEEAL RHYEDFPKLW MMKGQIEE Q KEMMEKAREA YNQGLKKCPH STPLWLLLSR LEEKIGQLTR ARAILEKSRL KNPKNPGLWL ESVRLEYRAG LKNIANTLM AKALQECPNS GILWSEAIFL EARPQRRTKS VDALKKCEHD PHVLLAVAKL FWSQRKITKA REWFHRTVKI DSDLGDAWAF FYKFELQHG TEEQQEEVRK RCESAEPRHG ELWCAVSKDI ANWQKKIGDI LRLVAGRIKN TF

UniProtKB: Pre-mRNA-processing factor 6

Macromolecule #5: Probable ATP-dependent RNA helicase DDX23

• Macromolecule: Name: Probable ATP-dependent RNA helicase DDX23 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 95.785148 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MAGELADKKD RDASPSKEER KRSRTPDRER DRDRDRKSSP SKDRKRHRSR DRRRGGSRSR SRSRSKSAER ERRHKERERD KERDRNKKD RDRDKDGHRR DKDRKRSSLS PGRGKDFKSR KDRDSKKDEE DEHGDKKPKA QPLSLEELLA KKKAEEEAEA K PKFLSKAE REAEALKRRQ QEVEERQRML EEERKKRKQF QDLGRKMLED PQERERRERR ERMERETNGN EDEEGRQKIR EE KDKSKEL HAIKERYLGG IKKRRRTRHL NDRKFVFEWD ASEDTSIDYN PLYKERHQVQ LLGRGFIAGI DLKQQKREQS RFY GDLMEK RRTLEEKEQE EARLRKLRKK EAKQRWDDRH WSQKKLDEMT DRDWRIFRED YSITTKGGKI PNPIRSWKDS SLPP HILEV IDKCGYKEPT PIQRQAIPIG LQNRDIIGVA ETGSGKTAAF LIPLLVWITT LPKIDRIEES DQGPYAIILA PTREL AQQI EEETIKFGKP LGIRTVAVIG GISREDQGFR LRMGCEIVIA TPGRLIDVLE NRYLVLSRCT YVVLDEADRM IDMGFE PDV QKILEHMPVS NQKPDTDEAE DPEKMLANFE SGKHKYRQTV MFTATMPPAV ERLARSYLRR PAVVYIGSAG KPHERVE QK VFLMSESEKR KKLLAILEQG FDPPIIIFVN QKKGCDVLAK SLEKMGYNAC TLHGGKGQEQ REFALSNLKA GAKDILVA T DVAGRGIDIQ DVSMVVNYDM AKNIEDYIHR IGRTGRAGKS GVAITFLTKE DSAVFYELKQ AILESPVSSC PPELANHPD AQHKPGTILT KKRREETIFA

UniProtKB: Probable ATP-dependent RNA helicase DDX23

Macromolecule #6: 116 kDa U5 small nuclear ribonucleoprotein component

• Macromolecule: Name: 116 kDa U5 small nuclear ribonucleoprotein component / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 109.560625 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MDTDLYDEFG NYIGPELDSD EDDDELGRET KDLDEMDDDD DDDDVGDHDD DHPGMEVVLH EDKKYYPTAE EVYGPEVETI VQEEDTQPL TEPIIKPVKT KKFTLMEQTL PVTVYEMDFL ADLMDNSELI RNVTLCGHLH HGKTCFVDCL IEQTHPEIRK R YDQDLCYT DILFTEQERG VGIKSTPVTV VLPDTKGKSY LFNIMDTPGH VNFSDEVTAG LRISDGVVLF IDAAEGVMLN TE RLIKHAV QERLAVTVCI NKIDRLILEL KLPPTDAYYK LRHIVDEVNG LISMYSTDEN LILSPLLGNV CFSSSQYSIC FTL GSFAKI YADTFGDINY QEFAKRLWGD IYFNPKTRKF TKKAPTSSSQ RSFVEFILEP LYKILAQVVG DVDTSLPRTL DELG IHLTK EELKLNIRPL LRLVCKKFFG EFTGFVDMCV QHIPSPKVGA KPKIEHTYTG GVDSDLGEAM SDCDPDGPLM CHTTK MYST DDGVQFHAFG RVLSGTIHAG QPVKVLGENY TLEDEEDSQI CTVGRLWISV ARYHIEVNRV PAGNWVLIEG VDQPIV KTA TITEPRGNEE AQIFRPLKFN TTSVIKIAVE PVNPSELPKM LDGLRKVNKS YPSLTTKVEE SGEHVILGTG ELYLDCV MH DLRKMYSEID IKVADPVVTF CETVVETSSL KCFAETPNKK NKITMIAEPL EKGLAEDIEN EVVQITWNRK KLGEFFQT K YDWDLLAARS IWAFGPDATG PNILVDDTLP SEVDKALLGS VKDSIVQGFQ WGTREGPLCD ELIRNVKFKI LDAVVAQEP LHRGGGQIIP TARRVVYSAF LMATPRLMEP YYFVEVQAPA DCVSAVYTVL ARRRGHVTQD APIPGSPLYT IKAFIPAIDS FGFETDLRT HTQGQAFSLS VFHHWQIVPG DPLDKSIVIR PLEPQPAPHL AREFMIKTRR RKGLSEDVSI SKFFDDPMLL E LAKQDVVL NYPM

UniProtKB: 116 kDa U5 small nuclear ribonucleoprotein component

Macromolecule #7: U5 small nuclear ribonucleoprotein 200 kDa helicase

• Macromolecule: Name: U5 small nuclear ribonucleoprotein 200 kDa helicase / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 244.823422 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MADVTARSLQ YEYKANSNLV LQADRSLIDR TRRDEPTGEV LSLVGKLEGT RMGDKAQRTK PQMQEERRAK RRKRDEDRHD INKMKGYTL LSEGIDEMVG IIYKPKTKET RETYEVLLSF IQAALGDQPR DILCGAADEV LAVLKNEKLR DKERRKEIDL L LGQTDDTR YHVLVNLGKK ITDYGGDKEI QNMDDNIDET YGVNVQFESD EEEGDEDVYG EVREEASDDD MEGDEAVVRC TL SANLVAS GELMSSKKKD LHPRDIDAFW LQRQLSRFYD DAIVSQKKAD EVLEILKTAS DDRECENQLV LLLGFNTFDF IKV LRQHRM MILYCTLLAS AQSEAEKERI MGKMEADPEL SKFLYQLHET EKEDLIREER SRRERVRQSR MDTDLETMDL DQGG EALAP RQVLDLEDLV FTQGSHFMAN KRCQLPDGSF RRQRKGYEEV HVPALKPKPF GSEEQLLPVE KLPKYAQAGF EGFKT LNRI QSKLYRAALE TDENLLLCAP TGAGKTNVAL MCMLREIGKH INMDGTINVD DFKIIYIAPM RSLVQEMVGS FGKRLA TYG ITVAELTGDH QLCKEEISAT QIIVCTPEKW DIITRKGGER TYTQLVRLII LDEIHLLHDD RGPVLEALVA RAIRNIE MT QEDVRLIGLS ATLPNYEDVA TFLRVDPAKG LFYFDNSFRP VPLEQTYVGI TEKKAIKRFQ IMNEIVYEKI MEHAGKNQ V LVFVHSRKET GKTARAIRDM CLEKDTLGLF LREGSASTEV LRTEAEQCKN LELKDLLPYG FAIHHAGMTR VDRTLVEDL FADKHIQVLV STATLAWGVN LPAHTVIIKG TQVYSPEKGR WTELGALDIL QMLGRAGRPQ YDTKGEGILI TSHGELQYYL SLLNQQLPI ESQMVSKLPD MLNAEIVLGN VQNAKDAVNW LGYAYLYIRM LRSPTLYGIS HDDLKGDPLL DQRRLDLVHT A ALMLDKNN LVKYDKKTGN FQVTELGRIA SHYYITNDTV QTYNQLLKPT LSEIELFRVF SLSSEFKNIT VREEEKLELQ KL LERVPIP VKESIEEPSA KINVLLQAFI SQLKLEGFAL MADMVYVTQS AGRLMRAIFE IVLNRGWAQL TDKTLNLCKM IDK RMWQSM CPLRQFRKLP EEVVKKIEKK NFPFERLYDL NHNEIGELIR MPKMGKTIHK YVHLFPKLEL SVHLQPITRS TLKV ELTIT PDFQWDEKVH GSSEAFWILV EDVDSEVILH HEYFLLKAKY AQDEHLITFF VPVFEPLPPQ YFIRVVSDRW LSCET QLPV SFRHLILPEK YPPPTELLDL QPLPVSALRN SAFESLYQDK FPFFNPIQTQ VFNTVYNSDD NVFVGAPTGS GKTICA EFA ILRMLLQSSE GRCVYITPME ALAEQVYMDW YEKFQDRLNK KVVLLTGETS TDLKLLGKGN IIISTPEKWD ILSRRWK QR KNVQNINLFV VDEVHLIGGE NGPVLEVICS RMRYISSQIE RPIRIVALSS SLSNAKDVAH WLGCSATSTF NFHPNVRP V PLELHIQGFN ISHTQTRLLS MAKPVYHAIT KHSPKKPVIV FVPSRKQTRL TAIDILTTCA ADIQRQRFLH CTEKDLIPY LEKLSDSTLK ETLLNGVGYL HEGLSPMERR LVEQLFSSGA IQVVVASRSL CWGMNVAAHL VIIMDTQYYN GKIHAYVDYP IYDVLQMVG HANRPLQDDE GRCVIMCQGS KKDFFKKFLY EPLPVESHLD HCMHDHFNAE IVTKTIENKQ DAVDYLTWTF L YRRMTQNP NYYNLQGISH RHLSDHLSEL VEQTLSDLEQ SKCISIEDEM DVAPLNLGMI AAYYYINYTT IELFSMSLNA KT KVRGLIE IISNAAEYEN IPIRHHEDNL LRQLAQKVPH KLNNPKFNDP HVKTNLLLQA HLSRMQLSAE LQSDTEEILS KAI RLIQAC VDVLSSNGWL SPALAAMELA QMVTQAMWSK DSYLKQLPHF TSEHIKRCTD KGVESVFDIM EMEDEERNAL LQLT DSQIA DVARFCNRYP NIELSYEVVD KDSIRSGGPV VVLVQLEREE EVTGPVIAPL FPQKREEGWW VVIGDAKSNS LISIK RLTL QQKAKVKLDF VAPATGAHNY TLYFMSDAYM GCDQEYKFSV DVKEAETDSD SD

UniProtKB: U5 small nuclear ribonucleoprotein 200 kDa helicase

Macromolecule #8: Small nuclear ribonucleoprotein F

• Macromolecule: Name: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 9.734171 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE

UniProtKB: Small nuclear ribonucleoprotein F

Macromolecule #9: Small nuclear ribonucleoprotein G

• Macromolecule: Name: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 8.508084 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MSKAHPPELK KFMDKKLSLK LNGGRHVQGI LRGFDPFMNL VIDECVEMAT SGQQNNIGMV VIRGNSIIML EALERV

UniProtKB: Small nuclear ribonucleoprotein G

Macromolecule #10: Small nuclear ribonucleoprotein Sm D1

• Macromolecule: Name: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.310653 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR EPVQLETLSI RGNNIRYFIL PDSLPLDTLL VDVEPKVKS KKREAVAGRG RGRGRGRGRG RGRGRGGPRR

UniProtKB: Small nuclear ribonucleoprotein Sm D1

Macromolecule #11: Small nuclear ribonucleoprotein Sm D2

• Macromolecule: Name: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.551928 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MSLLNKPKSE MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK KLLGRVKAFD RHCNMVLENV KEMWTEVPKS GKGKKKSKP VNKDRYISKM FLRGDSVIVV LRNPLIAGK

UniProtKB: Small nuclear ribonucleoprotein Sm D2

Macromolecule #12: Small nuclear ribonucleoprotein Sm D3

• Macromolecule: Name: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.940308 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ VYIRGSKIRF LILPDMLKNA PMLKSMKNK NQGSGAGRGK AAILKAQVAA RGRGRGMGRG NIFQKRR

UniProtKB: Small nuclear ribonucleoprotein Sm D3

Macromolecule #13: Small nuclear ribonucleoprotein-associated proteins B and B'

• Macromolecule: Name: Small nuclear ribonucleoprotein-associated proteins B and B'; type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 24.642131 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

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'

Macromolecule #14: Small nuclear ribonucleoprotein E

• Macromolecule: Name: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 10.817601 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MAYRGQGQKV QKVMVQPINL IFRYLQNRSR IQVWLYEQVN MRIEGCIIGF DEYMNLVLDD AEEIHSKTKS RKQLGRIMLK GDNITLLQS VSN

UniProtKB: Small nuclear ribonucleoprotein E

Macromolecule #3: U5 snRNA

• Macromolecule: Name: U5 snRNA / type: rna / ID: 3 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 37.254855 KDa

Sequence

String:

AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAU UUUUUGAGGC CUUGCUUUGG CAAGGCUA

GENBANK: GENBANK: AC105129.4

Macromolecule #15: GUANOSINE-5'-TRIPHOSPHATE

• Macromolecule: Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 1 / Formula: GTP
• Molecular weight: Theoretical: 523.18 Da

Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.8
• Grid: Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
• Specialist optics: Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Details: objective aperture 70um
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8506 / Average exposure time: 5.2 sec. / Average electron dose: 40.5 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 503581
• Startup model: Type of model: NONE
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 76918

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT

Output model

PDB-8q91:
Structure of the human 20S U5 snRNP core