[English] 日本語
Yorodumi
- EMDB-31330: The cryo-EM map of the DDX42-SF3b complex core region -

+
Open data


ID or keywords:

Loading...

-
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 / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / SAGA complex / U2 snRNP ...U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / SAGA complex / U2 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / precatalytic spliceosome / regulation of RNA splicing / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / positive regulation of transcription by RNA polymerase I / U2 snRNA binding / Cajal body / regulation of DNA repair / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / mRNA splicing, via spliceosome / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / nuclear matrix / intracellular protein localization / regulation of apoptotic process / RNA helicase activity / nuclear speck / RNA helicase / chromatin remodeling / mRNA binding / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
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 / : / PPP2R1A-like HEAT repeat ...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 / : / PPP2R1A-like HEAT repeat / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31330.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
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

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
Electron microscopy

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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more