[English] 日本語
Yorodumi
- EMDB-18222: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18222
TitleStructure of the hexameric CUL9-RBX1 complex with deletion of CUL9 ARM9 domain
Map datapostprocess
Sample
  • Complex: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 ARM9 domain
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
KeywordsCullin-RING Ubiquitin E3 Ligase / LIGASE
Function / homology
Function and homology information


cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity ...cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / regulation of mitotic nuclear division / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / post-translational protein modification / T cell activation / Regulation of BACH1 activity / cellular response to amino acid stimulus / Degradation of DVL / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / microtubule cytoskeleton organization / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RUNX2 expression and activity / cellular response to UV / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / DNA damage response / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain ...: / : / : / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin, conserved site / Cullin family signature. / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Ribosomal protein L2, domain 2 / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsHopf LVM / Horn-Ghetko D / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016European Union
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex.
Authors: Daniel Horn-Ghetko / Linus V M Hopf / Ishita Tripathi-Giesgen / Jiale Du / Sebastian Kostrhon / D Tung Vu / Viola Beier / Barbara Steigenberger / J Rajan Prabu / Luca Stier / Elias M Bruss / ...Authors: Daniel Horn-Ghetko / Linus V M Hopf / Ishita Tripathi-Giesgen / Jiale Du / Sebastian Kostrhon / D Tung Vu / Viola Beier / Barbara Steigenberger / J Rajan Prabu / Luca Stier / Elias M Bruss / Matthias Mann / Yue Xiong / Brenda A Schulman /
Abstract: Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with ...Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also called ROC1), of interest due to its tumor suppressive interaction with TP53, uniquely encompasses both cullin-RING and RBR domains. Here, cryo-EM, biochemistry and cellular assays elucidate a 1.8-MDa hexameric human CUL9-RBX1 assembly. Within one dimeric subcomplex, an E2-bound RBR domain is activated by neddylation of its own cullin domain and positioning from the adjacent CUL9-RBX1 in trans. Our data show CUL9 as unique among RBX1-bound cullins in dependence on the metazoan-specific UBE2F neddylation enzyme, while the RBR domain protects it from deneddylation. Substrates are recruited to various upstream domains, while ubiquitylation relies on both CUL9's neddylated cullin and RBR domains achieving self-assembled and chimeric cullin-RING/RBR E3 ligase activity.
History
DepositionAug 16, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18222.png

Downloads & links

-
Map

FileDownload / File: emd_18222.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 312 pix.
= 623.064 Å		2 Å/pix.
x 312 pix.
= 623.064 Å		2 Å/pix.
x 312 pix.
= 623.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.997 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0346
Minimum - Maximum-0.031313777 - 0.10507424
Average (Standard dev.)0.00020748319 (±0.005714108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 623.06396 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: refinement map

Fileemd_18222_additional_1.map
Annotationrefinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18222_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18222_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of the hexameric CUL9-RBX1 complex with deletion of CUL...

EntireName: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 ARM9 domain
Components
  • Complex: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 ARM9 domain
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1

-
Supramolecule #1: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL...

SupramoleculeName: Structure of the hexameric CUL9-RBX1 complex with deletion of CUL9 ARM9 domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cullin-9

MacromoleculeName: Cullin-9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVGERHAGDL MVPLGPRLQA YPEELIRQRP GHDGHPEYLI RWSVLKCGEV GKVGVEEGKA EHILMWLSAP EVYANCPGLL GERALSKGLQ HEPAGVSGSF PRDPGGLDEV AMGEMEADVQ ALVRRAARQL AESGTPSLTA AVLHTIHVLS AYASIGPLTG VFRETGALDL ...String:
MVGERHAGDL MVPLGPRLQA YPEELIRQRP GHDGHPEYLI RWSVLKCGEV GKVGVEEGKA EHILMWLSAP EVYANCPGLL GERALSKGLQ HEPAGVSGSF PRDPGGLDEV AMGEMEADVQ ALVRRAARQL AESGTPSLTA AVLHTIHVLS AYASIGPLTG VFRETGALDL LMHMLCNPEP QIRRSAGKML QALAAHDAGS RAHVLLSLSQ QDGIEQHMDF DSRYTLLELF AETTSSEEHC MAFEGIHLPQ IPGKLLFSLV KRYLCVTSLL DQLNSSPELG AGDQSSPCAT REKSRGQREL EFSMAVGNLI SELVRSMGWA RNLSEQGMSP PRPTRSIFQP YISGPSLLLP TIVTTPRRQG WVFRQRSEFS SRSGYGEYVQ QTLQPGMRVR MLDDYEEISA GDEGEFRQSN NGIPPVQVFW QSTGRTYWVH WHMLEILGPE EATEDKASAA VEKGAGATVL GTAFPSWDWN PMDGLYPLPY LQPEPQKNER VGYLTQAEWW ELLFFIKKLD LCEQQPIFQN LWKNLDETLG EKALGEISVS VEMAESLLQV LSSRFEGSTL NDLLNSQIYT KYGLLSNEPS SSSTSRNHSC TPDPEEESGS GSGSGSSEPP GSPERAALET PIIQGQDGSP ELLIRSLVGG PSAELLLDLE RVLCREGSPG GAVRPLLKRL QQETQPFLLL LRTLDAPGPN KTLLLSVLRV ITRLLDFPEA MVLPWHEVLE PCLNCLSGPS SDSEIVQELT CFLHRLASMH KDYAVVLCCL GAKEILSKVL DKHSAQLLLG CELRDLVTEC EKYAQLYSNL TSSILAGCIQ MVLGQIEDHR RTHQPINIPF FDVFLRHLCQ GSSVEVKEDK CWEKVEVSSN PHRASKLTDH NPKTYWESNG STGSHYITLH MHRGVLVRQL TLLVASEDSS YMPARVVVFG GDSTSCIGTE LNTVNVMPSA SRVILLENLN RFWPIIQIRI KRCQQGGIDT RVRGVEVLGP KPTFWPLFRE QLCRRTCLFY TIRAQAWSRD IAEDHRRLLQ LCPRLNRVLR HEQNFADRFL PDDEAAQALG KTCWEALVSP LVQNITSPDA EGVSALGWLL DQYLEQRETS RNPLSRAASF ASRVRRLCHL LVHVEPPPGP SPEPSTRPFS KNSKGRDRSP APSPVLPSSS LRNITQCWLS VVQEQVSRFL AAAWRAPDFV PRYCKLYEHL QRAGSELFGP RAAFMLALRS GFSGALLQQS FLTAAHMSEQ FARYIDQQIQ GGLIGGAPGV EMLGQLQRHL EPIMVLSGLE LATTFEHFYQ HYMADRLLSF GSSWLEGAVL EQIGLCFPNR LPQLMLQSLS TSEELQRQFH LFQLQRLDKL FLEQEDEEEK RLEEEEEEEE EEEAEKELFI EDPSPAISIL VLSPRCWPVS PLCYLYHPRK CLPTEFCDAL DRFSSFYSQS QNHPVLDMGP HRRLQWTWLG RAELQFGKQI LHVSTVQMWL LLKFNQTEEV SVETLLKDSD LSPELLLQAL VPLTSGNGPL TLHEGQDFPH GGVLRLHEPG PQRSGEALWL IPPQAYLNVE KDEGRTLEQK RNLLSCLLVR ILKAHGEKGL HIDQLVCLVL EAWQKGPNPP GTLGHTVAGG VACTSTDVLS CILHLLGQGY VKRRDDRPQI LMYAAPEPMG PCRGQADVPF CGSQSETSKP SPEAVATLAS LQLPAGRTMS PQEVEGLMKQ TVRQVQETLN LEPDVAQHLL AHSHWGAEQL LQSYSEDPEP LLLAAGLCVH QAQAVPVRPD HCPVCVSPLG CDDDLPSLCC MHYCCKSCWN EYLTTRIEQN LVLNCTCPIA DCPAQPTGAF IRAIVSSPEV ISKYEKALLR GYVESCSNLT WCTNPQGCDR ILCRQGLGCG TTCSKCGWAS CFNCSFPEAH YPASCGHMSQ WVDDGGYYDG MSVEAQSKHL AKLISKRCPS CQAPIEKNEG CLHMTCAKCN HGFCWRCLKS WKPNHKDYYN CSAMVSKAAR QEKRFQDYNE RCTFHHQARE FAVNLRNRVS AIHEVPPPRS FTFLNDACQG LEQARKVLAY ACVYSFYSQD AEYMDVVEQQ TENLELHTNA LQILLEETLL RCRDLASSLR LLRADCLSTG MELLRRIQER LLAILQHSAQ DFRVGLQSPS VEAWEAKGPN MPGSQPQASS GPEAEEEEED DEDDVPEWQQ DEFDEELDND SFSYDESENL DQETFFFGDE EEDEDEAYD

UniProtKB: Cullin-9

-
Macromolecule #2: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDVDTPSGTN SGAGKKRFEV KKWNAVALWA WDIVVDNCAI CRNHIMDLCI ECQANQ ASA TSEECTVAWG VCNHAFHFHC ISRWLKTRQV CPLDNREWEF QKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21505
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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