[English] 日本語
Yorodumi
- EMDB-55519: cryo-EM strucutre of CPSF160-WDR33-ZC3H18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55519
Titlecryo-EM strucutre of CPSF160-WDR33-ZC3H18
Map data
Sample
  • Complex: CPSF160-WDR33 core complex with ZC3H18
    • Complex: CPSF160-WDR33 core complex
      • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 1
      • Protein or peptide: pre-mRNA 3' end processing protein WDR33
    • Complex: ZC3H18
      • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH domain-containing protein 18
KeywordsZC3H18 / CPSF160 / WDR33 / Complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cap binding complex binding / RNA destabilization / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing ...co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cap binding complex binding / RNA destabilization / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / tRNA processing in the nucleus / DNA damage tolerance / RNA Polymerase II Transcription Termination / detection of maltose stimulus / maltose transport complex / carbohydrate transport / Processing of Capped Intron-Containing Pre-mRNA / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / fibrillar center / mRNA processing / outer membrane-bounded periplasmic space / spermatogenesis / protein-macromolecule adaptor activity / periplasmic space / nuclear speck / ribonucleoprotein complex / DNA damage response / enzyme binding / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
: / E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / Pre-mRNA 3' end processing protein Pfs2-like / Zinc finger, CCCH-type superfamily / zinc finger / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...: / E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / Pre-mRNA 3' end processing protein Pfs2-like / Zinc finger, CCCH-type superfamily / zinc finger / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Cleavage and polyadenylation specificity factor subunit 1 / Zinc finger CCCH domain-containing protein 18 / pre-mRNA 3' end processing protein WDR33
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsKuhn CC / Chand MK / Todesca S / Williams K / Keidel A / Garland W / Jensen TH / Conti E
Funding support Germany, European Union, Denmark, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)740329European Union
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Direct coupling of the human nuclear exosome adaptors NEXT and PAXT with transcription termination and processing machinerieswith transcription termination machineries
Authors: Kuhn CC / Chand MK / Todesca S / Williams K / Keidel A / Garland W / Jensen TH / Conti E
History
DepositionOct 30, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55519.png

Downloads & links

-
Map

FileDownload / File: emd_55519.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340.48 Å		0.85 Å/pix.
x 400 pix.
= 340.48 Å		0.85 Å/pix.
x 400 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.11113988 - 0.4172311
Average (Standard dev.)0.00017531494 (±0.00783864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.47998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_55519_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55519_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CPSF160-WDR33 core complex with ZC3H18

EntireName: CPSF160-WDR33 core complex with ZC3H18
Components
  • Complex: CPSF160-WDR33 core complex with ZC3H18
    • Complex: CPSF160-WDR33 core complex
      • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 1
      • Protein or peptide: pre-mRNA 3' end processing protein WDR33
    • Complex: ZC3H18
      • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH domain-containing protein 18

-
Supramolecule #1: CPSF160-WDR33 core complex with ZC3H18

SupramoleculeName: CPSF160-WDR33 core complex with ZC3H18 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: ZC3H18 uses two anchor points to interact with CPSF160
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: CPSF160-WDR33 core complex

SupramoleculeName: CPSF160-WDR33 core complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: ZC3H18

SupramoleculeName: ZC3H18 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cleavage and polyadenylation specificity factor subunit 1

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 161.074234 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYAVYKQAHP PTGLEFSMYC NFFNNSERNL VVAGTSQLYV YRLNRDAEAL TKNDRSTEGK AHREKLELAA SFSFFGNVMS MASVQLAGA KRDALLLSFK DAKLSVVEYD PGTHDLKTLS LHYFEEPELR DGFVQNVHTP RVRVDPDGRC AAMLVYGTRL V VLPFRRES ...String:
MYAVYKQAHP PTGLEFSMYC NFFNNSERNL VVAGTSQLYV YRLNRDAEAL TKNDRSTEGK AHREKLELAA SFSFFGNVMS MASVQLAGA KRDALLLSFK DAKLSVVEYD PGTHDLKTLS LHYFEEPELR DGFVQNVHTP RVRVDPDGRC AAMLVYGTRL V VLPFRRES LAEEHEGLVG EGQRSSFLPS YIIDVRALDE KLLNIIDLQF LHGYYEPTLL ILFEPNQTWP GRVAVRQDTC SI VAISLNI TQKVHPVIWS LTSLPFDCTQ ALAVPKPIGG VVVFAVNSLL YLNQSVPPYG VALNSLTTGT TAFPLRTQEG VRI TLDCAQ ATFISYDKMV ISLKGGEIYV LTLITDGMRS VRAFHFDKAA ASVLTTSMVT MEPGYLFLGS RLGNSLLLKY TEKL QEPPA SAVREAADKE EPPSKKKRVD ATAGWSAAGK SVPQDEVDEI EVYGSEAQSG TQLATYSFEV CDSILNIGPC ANAAV GEPA FLSEEFQNSP EPDLEIVVCS GHGKNGALSV LQKSIRPQVV TTFELPGCYD MWTVIAPVRK EEEDNPKGEG TEQEPS TTP EADDDGRRHG FLILSREDST MILQTGQEIM ELDTSGFATQ GPTVFAGNIG DNRYIVQVSP LGIRLLEGVN QLHFIPV DL GAPIVQCAVA DPYVVIMSAE GHVTMFLLKS DSYGGRHHRL ALHKPPLHHQ SKVITLCLYR DLSGMFTTES RLGGARDE L GGRSGPEAEG LGSETSPTVD DEEEMLYGDS GSLFSPSKEE ARRSSQPPAD RDPAPFRAEP THWCLLVREN GTMEIYQLP DWRLVFLVKN FPVGQRVLVD SSFGQPTTQG EARREEATRQ GELPLVKEVL LVALGSRQSR PYLLVHVDQE LLIYEAFPHD SQLGQGNLK VRFKKVPHNI NFREKKPKPS KKKAEGGGAE EGAGARGRVA RFRYFEDIYG YSGVFICGPS PHWLLVTGRG A LRLHPMAI DGPVDSFAPF HNVNCPRGFL YFNRQGELRI SVLPAYLSYD APWPVRKIPL RCTAHYVAYH VESKVYAVAT ST NTPCARI PRMTGEEKEF ETIERDERYI HPQQEAFSIQ LISPVSWEAI PNARIELQEW EHVTCMKTVS LRSEETVSGL KGY VAAGTC LMQGEEVTCR GRILIMDVIE VVPEPGQPLT KNKFKVLYEK EQKGPVTALC HCNGHLVSAI GQKIFLWSLR ASEL TGMAF IDTQLYIHQM ISVKNFILAA DVMKSISLLR YQEESKTLSL VSRDAKPLEV YSVDFMVDNA QLGFLVSDRD RNLMV YMYL PEAKESFGGM RLLRRADFHV GAHVNTFWRT PCRGATEGLS KKSVVWENKH ITWFATLDGG IGLLLPMQEK TYRRLL MLQ NALTTMLPHH AGLNPRAFRM LHVDRRTLQN AVRNVLDGEL LNRYLYLSTM ERSELAKKIG TTPDIILDDL LETDRVT AH F

UniProtKB: Cleavage and polyadenylation specificity factor subunit 1

-
Macromolecule #2: pre-mRNA 3' end processing protein WDR33

MacromoleculeName: pre-mRNA 3' end processing protein WDR33 / type: protein_or_peptide / ID: 2 / Details: N-terminal TwinStrep tag, C-terminal FLAG-tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.164035 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KTAGLEVLFQ GPDVPMATEI GSPPRFFHMP RFQHQAPRQL FYKRPDFAQQ QAMQQLTFD GKRMRKAVNR KTIDYNPSVI KYLENRIWQR DQRDMRAIQP DAGYYNDLVP PIGMLNNPMN AVTTKFVRTS T NKVKCPVF ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KTAGLEVLFQ GPDVPMATEI GSPPRFFHMP RFQHQAPRQL FYKRPDFAQQ QAMQQLTFD GKRMRKAVNR KTIDYNPSVI KYLENRIWQR DQRDMRAIQP DAGYYNDLVP PIGMLNNPMN AVTTKFVRTS T NKVKCPVF VVRWTPEGRR LVTGASSGEF TLWNGLTFNF ETILQAHDSP VRAMTWSHND MWMLTADHGG YVKYWQSNMN NV KMFQAHK EAIREASFSP TDNKFATCSD DGTVRIWDFL RCHEERILRG HGADVKCVDW HPTKGLVVSG SKDSQQPIKF WDP KTGQSL ATLHAHKNTV MEVKLNLNGN WLLTASRDHL CKLFDIRNLK EELQVFRGHK KEATAVAWHP VHEGLFASGG SDGS LLFWH VGVEKEVGGM EMAHEGMIWS LAWHPLGHIL CSGSNDHTSK FWTRNRPGDK MRDDYKDDDD K

UniProtKB: pre-mRNA 3' end processing protein WDR33

-
Macromolecule #3: Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Zinc finger CCCH domain-containing protein 18
type: protein_or_peptide / ID: 3
Details: sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, ...Details: sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830,sample post-3C-cleavage, fusion protein: ZC3H18_101-135-(GSGSGSGS)-ZC3H18_805-830
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.94675 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYAQ SGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA KGKSALMFNL Q EPYFTWPL ...String:
MHHHHHHGKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYAQ SGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA KGKSALMFNL Q EPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKHMNADTDY SIAEAAFNKG ETAMTINGPW AW SNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEAVNKDKPL GAVALKSYEE ELA KDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTNS SSNNNNTSLE VLFQGPDSMG DEGE EDRTS DLRDEASSVT RELDEHELDY DEEVPGSGSG SGSPQQGTFV AHKEIKLTLL NKAADKGSR

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Zinc finger CCCH domain-containing protein 18, Zinc finger CCCH domain-containing protein 18

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium cloride
5.0 mMMgCl2magnesium cloride
0.04 %14H28O6n-octyl-beta-d-glucoside

Details: 20mM HEPES pH 7.5, 150mM NaCl, 5mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1512004
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