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- EMDB-31330: The cryo-EM map of the DDX42-SF3b complex core region -

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Basic information

Entry
Database: EMDB / ID: EMD-31330
TitleThe cryo-EM map of the DDX42-SF3b complex core region
Map dataThe EM map of the DDX42-SF3b complex
Sample
  • Complex: The DDX42-SF3b core complex
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 1
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Protein or peptide: Splicing factor 3B subunit 3
    • Protein or peptide: ATP-dependent RNA helicase DDX42
  • Ligand: ZINC ION
KeywordsDDX32 / SF3B1 / SF3b / U2 snRNP / SPLICING
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / : / U2-type prespliceosome assembly / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / : / U2-type prespliceosome assembly / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / Cajal body / U2 snRNA binding / regulation of DNA repair / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / protein localization / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA splicing, via spliceosome / nuclear matrix / regulation of apoptotic process / RNA helicase activity / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term ...Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Armadillo-like helical / helicase superfamily c-terminal domain / 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 / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Splicing factor 3B subunit 1 / Splicing factor 3B subunit 3 / PHD finger-like domain-containing protein 5A / ATP-dependent RNA helicase DDX42 / Splicing factor 3B subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang X / Zhan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Structural insights into branch site proofreading by human spliceosome
Authors: Zhang X / Zhan X / Bian T / Yang F / Li P / Lu Y / Xing Z / Fan R / Zhang QC / Shi Y
History
DepositionMay 21, 2021-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31330.png

Downloads & links

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Map

FileDownload / File: emd_31330.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of the DDX42-SF3b complex
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.13312618 - 0.23510407
Average (Standard dev.)0.00012694583 (±0.00725337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The DDX42-SF3b core complex

EntireName: The DDX42-SF3b core complex
Components
  • Complex: The DDX42-SF3b core complex
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 1
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Protein or peptide: Splicing factor 3B subunit 3
    • Protein or peptide: ATP-dependent RNA helicase DDX42
  • Ligand: ZINC ION

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Supramolecule #1: The DDX42-SF3b core complex

SupramoleculeName: The DDX42-SF3b core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.149369 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

UniProtKB: Splicing factor 3B subunit 5

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Macromolecule #2: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.747867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDYKDDDD KASDEVDAGT MKSVNDQPSG NLPFLKPDDI QYFDKLLVDV DESTLSPEEQ KERKIMKLLL KIKNGTPPMR KAALRQITD KAREFGAGPL FNQILPLLMS PTLEDQERHL LVKVIDRILY KLDDLVRPYV HKILVVIEPL LIDEDYYARV E GREIISNL ...String:
MASDYKDDDD KASDEVDAGT MKSVNDQPSG NLPFLKPDDI QYFDKLLVDV DESTLSPEEQ KERKIMKLLL KIKNGTPPMR KAALRQITD KAREFGAGPL FNQILPLLMS PTLEDQERHL LVKVIDRILY KLDDLVRPYV HKILVVIEPL LIDEDYYARV E GREIISNL AKAAGLATMI STMRPDIDNM DEYVRNTTAR AFAVVASALG IPSLLPFLKA VCKSKKSWQA RHTGIKIVQQ IA ILMGCAI LPHLRSLVEI IEHGLVDEQQ KVRTISALAI AALAEAATPY GIESFDSVLK PLWKGIRQHR GKGLAAFLKA IGY LIPLMD AEYANYYTRE VMLILIREFQ SPDEEMKKIV LKVVKQCCGT DGVEANYIKT EILPPFFKHF WQHRMALDRR NYRQ LVDTT VELANKVGAA EIISRIVDDL KDEAEQYRKM VMETIEKIMG NLGAADIDHK LEEQLIDGIL YAFQEQTTED SVMLN GFGT VVNALGKRVK PYLPQICGTV LWRLNNKSAK VRQQAADLIS RTAVVMKTCQ EEKLMGHLGV VLYEYLGEEY PEVLGS ILG ALKAIVNVIG MHKMTPPIKD LLPRLTPILK NRHEKVQENC IDLVGRIADR GAEYVSAREW MRICFELLEL LKAHKKA IR RATVNTFGYI AKAIGPHDVL ATLLNNLKVQ ERQNRVCTTV AIAIVAETCS PFTVLPALMN EYRVPELNVQ NGVLKSLS F LFEYIGEMGK DYIYAVTPLL EDALMDRDLV HRQTASAVVQ HMSLGVYGFG CEDSLNHLLN YVWPNVFETS PHVIQAVMG ALEGLRVAIG PCRMLQYCLQ GLFHPARKVR DVYWKIYNSI YIGSQDALIA HYPRIYNDDK NTYIRYELDY IL

UniProtKB: Splicing factor 3B subunit 1

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Macromolecule #3: PHD finger-like domain-containing protein 5A

MacromoleculeName: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.427524 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIV NLGSSKTDLF YERKKYGFKK R

UniProtKB: PHD finger-like domain-containing protein 5A

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Macromolecule #4: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 138.949188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WSHPQFEKGG GSGGGSGGSA WSHPQFEKGS AAAMFLYNLT LQRATGISFA IHGNFSGTKQ QEIVVSRGKI LELLRPDPNT GKVHTLLTV EVFGVIRSLM AFRLTGGTKD YIVVGSDSGR IVILEYQPSK NMFEKIHQET FGKSGCRRIV PGQFLAVDPK G RAVMISAI ...String:
WSHPQFEKGG GSGGGSGGSA WSHPQFEKGS AAAMFLYNLT LQRATGISFA IHGNFSGTKQ QEIVVSRGKI LELLRPDPNT GKVHTLLTV EVFGVIRSLM AFRLTGGTKD YIVVGSDSGR IVILEYQPSK NMFEKIHQET FGKSGCRRIV PGQFLAVDPK G RAVMISAI EKQKLVYILN RDAAARLTIS SPLEAHKANT LVYHVVGVDV GFENPMFACL EMDYEEADND PTGEAAANTQ QT LTFYELD LGLNHVVRKY SEPLEEHGNF LITVPGGSDG PSGVLICSEN YITYKNFGDQ PDIRCPIPRR RNDLDDPERG MIF VCSATH KTKSMFFFLA QTEQGDIFKI TLETDEDMVT EIRLKYFDTV PVAAAMCVLK TGFLFVASEF GNHYLYQIAH LGDD DEEPE FSSAMPLEEG DTFFFQPRPL KNLVLVDELD SLSPILFCQI ADLANEDTPQ LYVACGRGPR SSLRVLRHGL EVSEM AVSE LPGNPNAVWT VRRHIEDEFD AYIIVSFVNA TLVLSIGETV EEVTDSGFLG TTPTLSCSLL GDDALVQVYP DGIRHI RAD KRVNEWKTPG KKTIVKCAVN QRQVVIALTG GELVYFEMDP SGQLNEYTER KEMSADVVCM SLANVPPGEQ RSRFLAV GL VDNTVRIISL DPSDCLQPLS MQALPAQPES LCIVEMGGTE KQDELGERGS IGFLYLNIGL QNGVLLRTVL DPVTGDLS D TRTRYLGSRP VKLFRVRMQG QEAVLAMSSR SWLSYSYQSR FHLTPLSYET LEFASGFASE QCPEGIVAIS TNTLRILAL EKLGAVFNQV AFPLQYTPRK FVIHPESNNL IIIETDHNAY TEATKAQRKQ QMAEEMVEAA GEDERELAAE MAAAFLNENL PESIFGAPK AGNGQWASVI RVMNPIQGNT LDLVQLEQNE AAFSVAVCRF SNTGEDWYVL VGVAKDLILN PRSVAGGFVY T YKLVNNGE KLEFLHKTPV EEVPAAIAPF QGRVLIGVGK LLRVYDLGKK KLLRKCENKH IANYISGIQT IGHRVIVSDV QE SFIWVRY KRNENQLIIF ADDTYPRWVT TASLLDYDTV AGADKFGNIC VVRLPPNTND EVDEDPTGNK ALWDRGLLNG ASQ KAEVIM NYHVGETVLS LQKTTLIPGG SESLVYTTLS GGIGILVPFT SHEDHDFFQH VEMHLRSEHP PLCGRDHLSF RSYY FPVKN VIDGDLCEQF NSMEPNKQKN VSEELDRTPP EVSKKLEDIR TRYAF

UniProtKB: Splicing factor 3B subunit 3

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Macromolecule #5: ATP-dependent RNA helicase DDX42

MacromoleculeName: ATP-dependent RNA helicase DDX42 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.261625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDYKDDDD KASDEVDAGT MNWNKGGPGT KRGFGFGGFA ISAGKKEEPK LPQQSHSAFG ATSSSSGFGK SAPPQLPSFY KIGSKRANF DEENAYFEDE EEDSSNVDLP YIPAENSPTR QQFHSKPVDS DSDDDPLEAF MAEVEDQAAR DMKRLEEKDK E RKNVKGIR ...String:
MASDYKDDDD KASDEVDAGT MNWNKGGPGT KRGFGFGGFA ISAGKKEEPK LPQQSHSAFG ATSSSSGFGK SAPPQLPSFY KIGSKRANF DEENAYFEDE EEDSSNVDLP YIPAENSPTR QQFHSKPVDS DSDDDPLEAF MAEVEDQAAR DMKRLEEKDK E RKNVKGIR DDIEEEDDQE AYFRYMAENP TAGVVQEEEE DNLEYDSDGN PIAPTKKIID PLPPIDHSEI DYPPFEKNFY NE HEEITNL TPQQLIDLRH KLNLRVSGAA PPRPGSSFAH FGFDEQLMHQ IRKSEYTQPT PIQCQGVPVA LSGRDMIGIA KTG SGKTAA FIWPMLIHIM DQKELEPGDG PIAVIVCPTR ELCQQIHAEC KRFGKAYNLR SVAVYGGGSM WEQAKALQEG AEIV VCTPG RLIDHVKKKA TNLQRVSYLV FDEADRMFDM GFEYQVRSIA SHVRPDRQTL LFSATFRKKI EKLARDILID PIRVV QGDI GEANEDVTQI VEILHSGPSK WNWLTRRLVE FTSSGSVLLF VTKKANAEEL ANNLKQEGHN LGLLHGDMDQ SERNKV ISD FKKKDIPVLV ATDVAARGLD IPSIKTVINY DVARDIDTHT HRIGRTGRAG EKGVAYTLLT PKDSNFAGDL VRNLEGA NQ HVSKELLDLA MQNAWFRKSR FKGGKGKKLN IGGGGLGYRE RPGLGSENMD RGNNNVMSNY EAYKPSTGAM GDRLTAMK A AFQSQYKSHF VAASLSNQKA GSSAAGASGW TSAGSLNSVP TNSAQQGHNS PDSPVTSAAK GIPGFGNTGN ISGAPVTYP SAGAQGVNNT ASGNNSREGT GGSNGKRERY TENRGSSRHS HGETGNRHSD SPRHGDGGRH GDGYRHPESS SRHTDGHRHG ENRHGGSAG RHGENRGAND GRNGESRKEA FNRESKMEPK MEPKVDSSKM DKVDSKTDKT ADGFAVPEPP KRKKSRWDS

UniProtKB: ATP-dependent RNA helicase DDX42

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / 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

Concentration1.5 mg/mL
BufferpH: 7.9
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234800

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