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- EMDB-53348: Cryo-EM structure of the core of the Arabidopsis thaliana UBR4/DI... -

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Basic information

Entry
Database: EMDB / ID: EMD-53348
TitleCryo-EM structure of the core of the Arabidopsis thaliana UBR4/DI19/CALM1 complex
Map data
Sample
  • Complex: Arabidopsis UBR4 complex
    • Protein or peptide: Auxin transport protein (BIG)
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: Protein DEHYDRATION-INDUCED 19
KeywordsUbiquitin ligase / Protein quality control / LIGASE
Function / homology
Function and homology information


calcium ion binding / zinc ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein dehydration-induced 19, C-terminal / Protein DEHYDRATION-INDUCED 19 / Stress-induced protein Di19, C-terminal / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 ...Protein dehydration-induced 19, C-terminal / Protein DEHYDRATION-INDUCED 19 / Stress-induced protein Di19, C-terminal / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Armadillo-like helical / EF-hand domain pair / Armadillo-type fold / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Auxin transport protein BIG / Calmodulin-1 / Protein DEHYDRATION-INDUCED 19
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGrabarczyk DB / Clausen T
Funding support Austria, European Union, 2 items
OrganizationGrant numberCountry
Austrian Research Promotion Agency852936 Austria
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: Science / Year: 2025
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.
Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee ...Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee / Jin Seok Shin / Anton Meinhart / Gijs A Versteeg / Eszter Zavodszky / Hyun Kyu Song / Ramanujan S Hegde / Tim Clausen /
Abstract: Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome ...Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome system, where UBR4 acts as an essential E4 ubiquitin ligase, amplifying degradation marks on defective proteins. Cryo-electron microscopy analysis of UBR4 in complex with its cofactors KCMF1 and CALM1 reveals a massive 1.3-megadalton ring structure, featuring a central substrate-binding arena and flexibly attached catalytic units. Our structure shows how UBR4 binds substrate and extends lysine-48-specific ubiquitin chains. Efficient substrate targeting depends on both preubiquitination and specific N-degrons, with KCMF1 acting as a key substrate filter. The architecture of the E4 megacomplex is conserved across eukaryotes, but species-specific adaptations allow UBR4 to perform its precisely tuned quality control function in diverse cellular environments.
History
DepositionApr 8, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53348.png

Downloads & links

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Map

FileDownload / File: emd_53348.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 384 pix.
= 486.912 Å		1.27 Å/pix.
x 384 pix.
= 486.912 Å		1.27 Å/pix.
x 384 pix.
= 486.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.4859945 - 0.91958576
Average (Standard dev.)0.00047953546 (±0.016894149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 486.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53348_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53348_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53348_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis UBR4 complex

EntireName: Arabidopsis UBR4 complex
Components
  • Complex: Arabidopsis UBR4 complex
    • Protein or peptide: Auxin transport protein (BIG)
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: Protein DEHYDRATION-INDUCED 19

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Supramolecule #1: Arabidopsis UBR4 complex

SupramoleculeName: Arabidopsis UBR4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Auxin transport protein (BIG)

MacromoleculeName: Auxin transport protein (BIG) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 572.67225 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADDLANLCR FLFDDTAFPS LSSSASSDLF SRRLRSDDSI KRGLRSFYLL LRWGVAPIGG DDADSSGKLR FETWSDSQLQ ALVSISQAI LLLSRSLLVD QLEPIVLGVI QEVMEFSLSF LEKSSFRQND LKMEINMEIL LEIASFDGSE KQYDILPDFS P AEVAELWP ...String:
MADDLANLCR FLFDDTAFPS LSSSASSDLF SRRLRSDDSI KRGLRSFYLL LRWGVAPIGG DDADSSGKLR FETWSDSQLQ ALVSISQAI LLLSRSLLVD QLEPIVLGVI QEVMEFSLSF LEKSSFRQND LKMEINMEIL LEIASFDGSE KQYDILPDFS P AEVAELWP AFSGEHDNMD AQSLVKCTFQ GGRCSNEEKP VDRLLITLMS ECIESDVQAQ SVVKSPFQQD CGDLNPFTRH LA VVHLRCV CRLIMVCKEL VQLPNMLDEK TVDQAVLDKL SFCLRILKLL GSLSKDVQSI ENDGSLLQAV ASFTDAFPKL FRV FFEFTN HTATEGNIES LSLALVEGFL NLVQLIFGKS SVFQNVQACV AASIVSNLDS SVWRYDGSSC NLTPPLAYFP RSVI YTLKL IQDLKRQPYH IHDLRVLESE VTYEDVSSTV DSVYFHLRQE KIPLLKCFTV EDIMRVIFPS SSQWMDNFFH LVYFL HREG VKLRPKVERT YSSLRSNSFA EVESQISHDD EALFGNLFSE GSRSLCSIEP NDQPPVSVSS NLLLQAAKEL LNFLRA CIL CQEWVPSIYE DGCKKLDTGH IDILLNIVGC SIEDKASDGG CMLQDEGRPG HVAFELLLNL LRSRALSDFL ESYLFQQ IL VVENSDFNYN DKTLALLAHT LLCRPGLAGA QLRAKIYDGF VSFVTERARG ICAEALSLKE LTACLPSAFH IEILLMAF H LSNEAEKAKF SNLIASCLHK VDTPAGICDG PQLSSWAMLI SRLLVLLHHM LLHPNTCPTS LMLDLRSKLR EVRSCGSNL HVTVGDHLSS WASLVARGIT DSWAEDESVS HLMSQMIDFS PHPPTFQNDV STAKTLNLDY GDLSASLCRV LGLWKGKKAG KVEDLLVER YIFMLSSDIA RINCALDSQP SLHVNYQNVD ISNSVDLIST SHLLVGDINV VGRNIELRNI LIGVLNQLQA A PEQVVEDL GWDYIREGAW LSLLLYFLDG GVWDYCNKNS CSEIDPFWKE CTSVDAKYVA AAEGVVSYLM KTGDIAELLR ML SSLVGKY LRVYKKAFLA TFSDWNHHGH SSPSLLLLKH TQFGKSLQGE YAKIGDNSLH LQCIFYLSKL DSLGDGRGSG VLW KVFWEF MVHGFPTSLQ TSSAILLSCI LSIRCIVLTI NGLLKLGNSK EKFGVDTSVL HQLLDSIMII KFDQVFESFH GKCE EIHQN ICAVLQLPDL TELFLMKDME GFVRDISAEQ IDRSQVLEGV ITKIVDVMDS LSKDSSKSDI FKFYLGVDAV SEHTR EFYE LQRGDLSVFI DSLDYCSLEP VNIKVLNFLV DLLSVAQSPD LRRRVQQKFI DMDLISLSGW LERRLLGSFV EEIDGK KTA KGNSLPFREA AMNFINCLVS STNDLQTREL QNHLFEALLI SLDTAFLSFD IHMSMSYFHF VLQLAREDNL MKMVLKR TI MLMEKLAAEE KLLPGLKFIF GVIGTLLSNR SPSHGESLCG KSLASYKNTA TGPLVPKLSG TTKKSDTLAL PVDQEGSS I SLECDVTSVD EDEDDGTSDG EVASLDKEDE EDANSERYLA SKVCTFTSSG SNFMEQHWYF CYTCDLTVSK GCCSVCAKV CHRGHRVVYS RSSRFFCDCG AGGVRGSSCQ CLKPRKYNGN GSAPARGTNN FQSFLPLSED ADQLGESDSD VEEDGFGEEN HVVLYIPKE TQYKMSLLLE ELGIEDRVLE LFSSLLPSIT SKRDSGLSKE KQVNLGKDKV LSFDTDLLQL KKAYKSGSLD L KIKADYTN SKDLKSLLAN GSLVKSLLSV SVRGRLAVGE GDKVAIFDVG QLIGQATIAP INADKANVKP LSRNIVRFEI VH LSFNPVV ENYLAVAGLE DCQILTLNHR GEVIDRLAVE LALQGAFIRR IDWVPGSQVQ LMVVTNKFVK IYDLSQDSIS PTQ YFTLPN DMIVDATLFV ASRGRVFLLV LSEQGNLYRF ELSWGGNAGA TPLKEIVQIM GKDVTGKGSS VYFSPTYRLL FISY HDGSS FMGRLSSDAT SLTDTSGMFE EESDCKQRVA GLHRWKELLA GSGLFICFSS VKSNAVLAVS LRGDGVCAQN LRHPT GSSS PMVGITAYKP LSKDNVHCLV LHDDGSLQIY SHVRSGVDTD SNFTAEKVKK LGSKILNNKT YAGAKPEFPL DFFERA FCI TADVRLGSDA IRNGDSEGAK QSLASEDGFI ESPSPVGFKI SVSNPNPDIV MVGIRMHVGT TSASSIPSEV TIFQRSI KM DEGMRCWYDI PFTVAESLLA DEDVVISVGP TTSGTALPRI DSLEVYGRAK DEFGWKEKMD AVLDMEARVL GHGLLLPG S SKKRALAQSA SMEEQVIADG LKLLSIYYSV CRPRQEVVLS ELKCKQLLET IFESDRETLL QTTACRVLQS VFPRKEIYY QVKDTMRLLG VVKVTSILSS RLGILGTGGS IVEEFNAQMR AVSKVALTRK SNFSVFLEMN GSEVVDNLMQ VLWGILESEP LDTPTMNNV VMSSVELIYS YAECLASQGK DTGVHSVAPA VQLLKALMLF PNESVQTSSS LAISSRLLQV PFPKQTMLTT D DLVDNVTT PSVPIRTAGG NTHVMIEEDS ITSSVQYCCD GCSTVPILRR RWHCTVCPDF DLCEACYEVL DADRLPPPHT RD HPMTAIP IEVESLGADT NEIQFSADEV GISNMLPVVT SSIPQASTPS IHVLEPGESA EFSASLTDPI SISASKRAVN SLI LSEFLQ ELSGWMETVS GVQAIPVMQL FYRLSSAIGG AFMDSSKPEE ISLDKLIKWL LGEINLSKPF AASTRSSLGE IVIL VFMFF TLMLRSWHQP GSDGSSSKLG GSTDVHDRRI VQSSTVVATQ SSLHVQERDD FASQLVRACS CLRNQEFVNY LMNIL QQLV HVFKSRAANV EARGSSSGSG CGAMLTVRRD LPAGNYSPFF SDSYAKAHRA DIFVDYHRLL LENVFRLVYT LVRPEK QEK MGEKEKVYRN ASSKDLKLDG FQDVLCSYIN NPHTAFVRRY ARRLFLHLCG SKTQYYSVRD SWQFSNEVKN LYKHVEK SG GFENNVSYER SVKIVKSLST IAEVAVARPR NWQKYCLRHG DFLSFLLNGV FHFAEESVIQ TLKLLNLAFY QGKDVSSS V QKAEATEVVT GSNRSGSQSV DSKKKKKGED GHDSGLEKLY VDMEGVVDIF SANCGDLLRQ FIDFFLLEWN SSSVRTEAK SVIYGLWHHG RHSFKESLLA ALLQKVRYLP AYGQNIVEYT ELVSLLLDKA PENNSKQAIN ELVDRCLNPD VIRCFFETLH SQNELIANH PNSRIYSTLG NLVEFDGYYL ESEPCVACSS PDVPYSKMKL ESLKSETKFT DNRIIVKCTG SYTIQSVTMN V HDARKSKS VKVLNLYYNN RPVSDLSELK NNWSLWKRAK SCHLSFNQTE LKVEFPIPIT ACNFMIELDS FYENLQALSL EP LQCPRCS RPVTDKHGIC SNCHENAYQC RQCRNINYEN LDSFLCNECG YSKYGRFEFN FMAKPSFIFD NMENDEDMKK GLA AIESES ENAHKRYQQL LGFKKPLLKI VSSIGETEMD SQHKDTVQQM MASLPGPSCK INRKIALLGV LYGEKCKAAF DSVS KSVQT LQGLRRVLMS YLHQKNSNFS SGASRCVVSK TPNNCYGCAT TFVTQCLEIL QVLSKHPRSR KQLVAAGILS ELFEN NIHQ GPKTARAQAR AALSTFSEGD LSAVNELNNL VQKKIMYCLE HHRSMDIALA TREEMLLLSE VCSLTDEFWE SRLRLV FQL LFSSIKLGAK HPAISEHIIL PCLKIISVAC TPPKPDTAEK EQTMGKSAPA VQEKDENAAG VIKYSSESEE NNLNVSQ KT RDIQLVSYLE WEKGASYLDF VRRQYKASQS IRGASQKSRT HRSDFLALKY TLRWKRRSSR TSKGGLQAFE LGSWVTEL I LSACSQSIRS EMCTLISLLA AQSSPRRYRL INLLIGLLPA TLAAGESSAE YFELLFKMIE TQDALLFLTV RGCLTTICK LISQEVGNIE SLERSLQIDI SQGFTLHKLL ELLGKFLEVP NIRSRFMRDN LLSHVLEALI VIRGLIVQKT KLINDCNRRL KDLLDGLLL ESSENKRQFI RACVSGLQTH AEENKGRTCL FILEQLCNLI CPSKPEAVYM LILNKSHTQE EFIRGSMTKN P YSSAEIGP LMRDVKNKIC QQLDLLGLLE DDYGMELLVA GNIISLDLSI AQVYELVWKK SNQSSTSLTN SALLASNAAP SR DCPPMTV TYRLQGLDGE ATEPMIKELE EDREESQDPE IEFAIAGAVR EYGGLEILLD MIKSLQDDFK SNQEEMVAVL DLL NHCCKI RENRRALLRL GALSLLLETA RRAFSVDAME PAEGILLIVE SLTLEANESD SISAAQSALT VSNEETGTWE QAKK IVLMF LERLSHPSGL KKSNKQQRNT EMVARILPYL TYGEPAAMEA LIEHFSPYLQ NWSEFDQLQQ RHEEDPKDDS IAQQA AKQR FTVENFVRVS ESLKTSSCGE RLKDIVLENG IIAVAVKHIK EIFAITGQTG FKSSKEWLLA LKLPSVPLIL SMLRGL SMG HLPTQTCIDE GGILTLLHAL EGVSGENDIG ARAENLLDTL ADKEGKGDGF LGEKVRALRD ATKDEMRRRA LRKREEL LQ GLGMRQELSS DGGERIVVSQ PILEGFEDVE EEEDGLACMV CREGYKLRPS DLLGVYSYSK RVNLGVGNSG SARGECVY T TVSYFNIIHF QCHQEAKRAD AALKNPKKEW EGAMLRNNES LCNSLFPVKG PSVPLAQYLR YVDQYWDNLN ALGRADGSR LRLLTYDIVL MLARFATGAS FSADCRGGGR DSNSRFLPFM FQMARHLLDQ GGPVQRTNMA RSVSSYISSS STSTATAPSS DSRPLTPGS QLSSTGTEET VQFMMVNSLL SESYESWLQH RRVFLQRGIY HTFMQHAHGR VASRAAEPTS SGGKTQDAET L TGDELLSI VKPMLVYTGM IEQLQQLFKP KKPVHIEPIK KEGTSSGVEL EPWEIVMKEK LLNVKEMIGF SKELISWLDE IN SATDLQE AFDIVGVLAD VLSEGVTQCD QFVRSAIDKD GSLEVLFQGP AEAAAKEAAA KEAAAKEAAA KALEAEAAAK EAA AKEAAA KEAAAKAHHH HHHHH

UniProtKB: Auxin transport protein BIG

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.042893 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDYKDHDGDY KDHDIDYKDD DDKGGSGGMA DQLTDEQISE FKEAFSLFDK DGDGCITTKE LGTVMRSLGQ NPTEAELQDM INEVDADGN GTIDFPEFLN LMAKKMKDTD SEEELKEAFR VFDKDQNGFI SAAELRHVMT NLGEKLTDEE VEEMIREADV D GDGQINYE EFVKIMMAK

UniProtKB: Calmodulin-1

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Macromolecule #3: Protein DEHYDRATION-INDUCED 19

MacromoleculeName: Protein DEHYDRATION-INDUCED 19 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.828037 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDADSKRFLA TLRSRSEMLM GFEEIDGDDD FQEEFACPFC AESYDIIGLC CHIDDEHTLE SKNAVCPVCS LKVGVDIVAH ITLHHGSLF KLQRKRKSRK SGTNSTLSLL RKELREGDLQ RLLGFTSRNG SVASSVTPDP LLSSFISPTR SQSSPAPRQT K NVSEDKQI ...String:
MDADSKRFLA TLRSRSEMLM GFEEIDGDDD FQEEFACPFC AESYDIIGLC CHIDDEHTLE SKNAVCPVCS LKVGVDIVAH ITLHHGSLF KLQRKRKSRK SGTNSTLSLL RKELREGDLQ RLLGFTSRNG SVASSVTPDP LLSSFISPTR SQSSPAPRQT K NVSEDKQI ERKRQVFISP VSLKDREERR HKSEFVQRLL SSAIFDEVGG SGGSAWSHPQ FEK

UniProtKB: Protein DEHYDRATION-INDUCED 19

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67226
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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