[English] 日本語
Yorodumi
- EMDB-11054: Linear Ubiquitin Chain Assembly Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11054
TitleLinear Ubiquitin Chain Assembly Complex
Map data3D refined model of LUBAC obtained from negative staining EM data.
Sample
  • Complex: Ternary complex of HOIP, HOIL-1L, and SHARPIN
    • Protein or peptide: HOIL-1L Interacting Protein
    • Protein or peptide: Heme-oxidized IRP2 ubiquitin ligase 1
    • Protein or peptide: Shank-associated RH domain-interacting protein
Function / homology
Function and homology information


apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway ...apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / keratinization / polyubiquitin modification-dependent protein binding / protein sequestering activity / mitochondrion organization / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / negative regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / defense response to bacterium / synapse / dendrite / protein-containing complex binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Sharpin, PH domain / Sharpin PH domain / : / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain ...Sharpin, PH domain / Sharpin PH domain / : / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain profile. / Ubiquitin-like domain / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
RanBP-type and C3HC4-type zinc finger-containing protein 1 / Sharpin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsRodriguez Carvajal A / Ikeda F / Haselbach D
Funding support Austria, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)614711 Austria
Austrian Science FundP 2550 8 Austria
CitationJournal: Elife / Year: 2021
Title: The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains.
Authors: Alan Rodriguez Carvajal / Irina Grishkovskaya / Carlos Gomez Diaz / Antonia Vogel / Adar Sonn-Segev / Manish S Kushwah / Katrin Schodl / Luiza Deszcz / Zsuzsanna Orban-Nemeth / Shinji ...Authors: Alan Rodriguez Carvajal / Irina Grishkovskaya / Carlos Gomez Diaz / Antonia Vogel / Adar Sonn-Segev / Manish S Kushwah / Katrin Schodl / Luiza Deszcz / Zsuzsanna Orban-Nemeth / Shinji Sakamoto / Karl Mechtler / Philipp Kukura / Tim Clausen / David Haselbach / Fumiyo Ikeda /
Abstract: The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear/Met1-linked ubiquitin chain formation. One of the LUBAC components, heme-oxidized IRP2 ubiquitin ...The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear/Met1-linked ubiquitin chain formation. One of the LUBAC components, heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L), was recently shown to catalyse oxyester bond formation between ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. Here, we present the first 3D reconstruction of human LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that this event depends on HOIL-1L catalytic activity. By cross-linking mass spectrometry showing proximity between the catalytic RING-in-between-RING (RBR) domains, a coordinated ubiquitin relay mechanism between the HOIL-1-interacting protein (HOIP) and HOIL-1L ligases is suggested. In mouse embryonic fibroblasts, these heterotypic chains were induced by TNF, which is reduced in cells expressing an HOIL-1L catalytic inactive mutant. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains by the concerted action of HOIP and HOIL-1L.
History
DepositionMay 19, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11054.png

Downloads & links

-
Map

FileDownload / File: emd_11054.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined model of LUBAC obtained from negative staining EM data.
Voxel sizeX=Y=Z: 3.7 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.052657463 - 0.1393197
Average (Standard dev.)0.0007289691 (±0.01032264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 333.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z333.000333.000333.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-0.0530.1390.001

-
Supplemental data

-
Sample components

-
Entire : Ternary complex of HOIP, HOIL-1L, and SHARPIN

EntireName: Ternary complex of HOIP, HOIL-1L, and SHARPIN
Components
  • Complex: Ternary complex of HOIP, HOIL-1L, and SHARPIN
    • Protein or peptide: HOIL-1L Interacting Protein
    • Protein or peptide: Heme-oxidized IRP2 ubiquitin ligase 1
    • Protein or peptide: Shank-associated RH domain-interacting protein

-
Supramolecule #1: Ternary complex of HOIP, HOIL-1L, and SHARPIN

SupramoleculeName: Ternary complex of HOIP, HOIL-1L, and SHARPIN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Full length proteins.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightExperimental: 222 KDa

-
Macromolecule #1: HOIL-1L Interacting Protein

MacromoleculeName: HOIL-1L Interacting Protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGEEEERAF LVAREELASA LRRDSGQAFS LEQLRPLLAS SLPLAARYLQ LDAARLVRCN AHGEPRNYLN TLSTALNIL EKYGRNLLSP QRPRYWRGVK FNNPVFRSTV DAVQGGRDVL RLYGYTEEQP DGLSFPEGQE E PDEHQVAT VTLEVLLLRT ELSLLLQNTH ...String:
MPGEEEERAF LVAREELASA LRRDSGQAFS LEQLRPLLAS SLPLAARYLQ LDAARLVRCN AHGEPRNYLN TLSTALNIL EKYGRNLLSP QRPRYWRGVK FNNPVFRSTV DAVQGGRDVL RLYGYTEEQP DGLSFPEGQE E PDEHQVAT VTLEVLLLRT ELSLLLQNTH PRQQALEQLL EDKVEDDMLQ LSEFDPLLRE IAPGPLTTPS VP GSTPGPC FLCGSAPGTL HCPSCKQALC PACDHLFHGH PSRAHHLRQT LPGVLQGTHL SPSLPASAQP RPQ STSLLA LGDSSLSSPN PASAHLPWHC AACAMLNEPW AVLCVACDRP RGCKGLGLGT EGPQGTGGLE PDLA RGRWA CQSCTFENEA AAVLCSICER PRLAQPPSLV VDSRDAGICL QPLQQGDALL ASAQSQVWYC IHCTF CNSS PGWVCVMCNR TSSPIPAQHA PRPYASSLEK GPPKPGPPRR LSAPLPSSCG DPEKQRQDKM REEGLQ LVS MIREGEAAGA CPEEIFSALQ YSGTEVPLQW LRSELPYVLE MVAELAGQQD PGLGAFSCQE ARRAWLD RH GNLDEAVEEC VRTRRRKVQE LQSLGFGPEE GSLQALFQHG GDVSRALTEL QRQRLEPFRQ RLWDSGPE P TPSWDGPDKQ SLVRRLLAVY ALPSWGRAEL ALSLLQETPR NYELGDVVEA VRHSQDRAFL RRLLAQECA VCGWALPHNR MQALTSCECT ICPDCFRQHF TIALKEKHIT DMVCPACGRP DLTDDTQLLS YFSTLDIQLR ESLEPDAYA LFHKKLTEGV LMRDPKFLWC AQCSFGFIYE REQLEATCPQ CHQTFCVRCK RQWEEQHRGR S CEDFQNWK RMNDPEYQAQ GLAMYLQENG IDCPKCKFSY ALARGGCMHF HCTQCRHQFC SGCYNAFYAK NK CPEPNCR VKKSLHGHHP RDCLFYLRDW TALRLQKLLQ DNNVMFNTEP PAGARAVPGG GCRVIEQKEV PNG LRDEAC GKETPAGYAG LCQAHYKEYL VSLINAHSLD PATLYEVEEL ETATERYLHV RPQPLAGEDP PAYQ ARLLQ KLTEEVPLGQ SIPRRRK

-
Macromolecule #2: Heme-oxidized IRP2 ubiquitin ligase 1

MacromoleculeName: Heme-oxidized IRP2 ubiquitin ligase 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEKTKKAEE MALSLTRAVA GGDEQVAMKC AIWLAEQRVP LSVQLKPEVS PTQDIRLWVS VEDAQMHTVT IWLTVRPDM TVASLKDMVF LDYGFPPVLQ QWVIGQRLAR DQETLHSHGV RQNGDSAYLY LLSARNTSLN P QELQRERQ LRMLEDLGFK DLTLQPRGPL ...String:
MDEKTKKAEE MALSLTRAVA GGDEQVAMKC AIWLAEQRVP LSVQLKPEVS PTQDIRLWVS VEDAQMHTVT IWLTVRPDM TVASLKDMVF LDYGFPPVLQ QWVIGQRLAR DQETLHSHGV RQNGDSAYLY LLSARNTSLN P QELQRERQ LRMLEDLGFK DLTLQPRGPL EPGPPKPGVP QEPGRGQPDA VPEPPPVGWQ CPGCTFINKP TR PGCEMCC RARPEAYQVP ASYQPDEEER ARLAGEEEAL RQYQQRKQQQ QEGNYLQHVQ LDQRSLVLNT EPA ECPVCY SVLAPGEAVV LRECLHTFCR ECLQGTIRNS QEAEVSCPFI DNTYSCSGKL LEREIKALLT PEDY QRFLD LGISIAENRS AFSYHCKTPD CKGWCFFEDD VNEFTCPVCF HVNCLLCKAI HEQMNCKEYQ EDLAL RAQN DVAARQTTEM LKVMLQQGEA MRCPQCQIVV QKKDGCDWIR CTVCHTEICW VTKGPRWGPG GPGDTS GGC RCRVNGIPCH PSCQNCH

-
Macromolecule #3: Shank-associated RH domain-interacting protein

MacromoleculeName: Shank-associated RH domain-interacting protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAPPAGGAAA AASDLGSAAV LLAVHAAVRP LGAGPDAEAQ LRRLQLSADP ERPGRFRLEL LGAGPGAVNL EWPLESVSY TIRGPTQHEL QPPPGGPGTL SLHFLNPQEA QRWAVLVRGA TVEGQNGSKS NSPPALGPEA C PVSLPSPP EASTLKGPPP EADLPRSPGN ...String:
MAPPAGGAAA AASDLGSAAV LLAVHAAVRP LGAGPDAEAQ LRRLQLSADP ERPGRFRLEL LGAGPGAVNL EWPLESVSY TIRGPTQHEL QPPPGGPGTL SLHFLNPQEA QRWAVLVRGA TVEGQNGSKS NSPPALGPEA C PVSLPSPP EASTLKGPPP EADLPRSPGN LTEREELAGS LARAIAGGDE KGAAQVAAVL AQHRVALSVQ LQ EACFPPG PIRLQVTLED AASAASAASS AHVALQVHPH CTVAALQEQV FSELGFPPAV QRWVIGRCLC VPE RSLASY GVRQDGDPAF LYLLSAPREA PATGPSPQHP QKMDGELGRL FPPSLGLPPG PQPAASSLPS PLQP SWSCP SCTFINAPDR PGCEMCSTQR PCTWDPLAAA ST

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
100.0 mMKClpotassium chloride
StainingType: NEGATIVE / Material: Uranyl acetate
GridMaterial: COPPER/PALLADIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN / Pretreatment - Pressure: 0.01 kPa
DetailsThis specimen was monodisperse. Specimen was run over S200 gel filtration column prior to staining.

-
Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: OTHER / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 35000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 33000 / Software - Name: RELION (ver. 3.1)

+
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://pdbjlvh1.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