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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | The cryo-EM map of the DDX42-SF3b complex core region | |||||||||
![]() | The EM map of the DDX42-SF3b complex | |||||||||
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![]() | DDX32 / SF3B1 / SF3b / U2 snRNP / SPLICING | |||||||||
Function / homology | ![]() 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 ...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 / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / U2 snRNA binding / regulation of DNA repair / Cajal body / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / protein localization / nuclear matrix / mRNA splicing, via spliceosome / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
![]() | Zhang X / Zhan X | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.2 KB 17.2 KB | Display Display | ![]() |
Images | ![]() | 87.6 KB | ||
Filedesc metadata | ![]() | 7.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 584 KB | Display | ![]() |
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Full document | ![]() | 583.5 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7evnMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | The EM map of the DDX42-SF3b complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : The DDX42-SF3b core complex
Entire | Name: The DDX42-SF3b core complex |
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Components |
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-Supramolecule #1: The DDX42-SF3b core complex
Supramolecule | Name: The DDX42-SF3b core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Splicing factor 3B subunit 5
Macromolecule | Name: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.149369 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN UniProtKB: Splicing factor 3B subunit 5 |
-Macromolecule #2: Splicing factor 3B subunit 1
Macromolecule | Name: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 98.747867 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: PHD finger-like domain-containing protein 5A
Macromolecule | Name: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.427524 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIV NLGSSKTDLF YERKKYGFKK R UniProtKB: PHD finger-like domain-containing protein 5A |
-Macromolecule #4: Splicing factor 3B subunit 3
Macromolecule | Name: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 138.949188 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #5: ATP-dependent RNA helicase DDX42
Macromolecule | Name: ATP-dependent RNA helicase DDX42 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 105.261625 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.9 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen 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
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234800 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |