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- EMDB-70612: Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-P... -

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Basic information

Entry
Database: EMDB / ID: EMD-70612
TitleCryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1)
Map dataUnsharpened 3D map of N8-CRL5-PCMTD1
Sample
  • Complex: Neddylated complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (N8-CRL5-PCMTD1)
    • Protein or peptide: Protein-L-isoaspartate O-methyltransferase domain-containing protein 1
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
KeywordsCUL5-RING ubiquitin ligase complex / PROTEIN BINDING
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / Inactivation of CSF3 (G-CSF) signaling / ERBB2 signaling pathway / regulation of neuron migration / Neddylation / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / target-directed miRNA degradation ...radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / Inactivation of CSF3 (G-CSF) signaling / ERBB2 signaling pathway / regulation of neuron migration / Neddylation / reelin-mediated signaling pathway / cullin-RING-type E3 NEDD8 transferase / target-directed miRNA degradation / VCB complex / elongin complex / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / intrinsic apoptotic signaling pathway in response to oxidative stress / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / apoptotic mitochondrial changes / ubiquitin ligase complex scaffold activity / cullin family protein binding / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / intrinsic apoptotic signaling pathway / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / calcium channel activity / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / Downregulation of ERBB2 signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / signaling receptor activity / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Elongin-C / Cullin family signature. / Elongin B ...Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Elongin-C / Cullin family signature. / Elongin B / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Elongin-C / Elongin-B / Cullin-5 / Protein-L-isoaspartate O-methyltransferase domain-containing protein 1 / RING-box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.72 Å
AuthorsPang EZ / Zhao B / Flowers C / Oroudjeva E / Winters JB / Pandey V / Sawaya MR / Wohlschlegel W / Loo JA / Rodriguez JA / Clarke SG
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM136614 United States
National Science Foundation (NSF, United States)MCB-1714569 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR028893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145286 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM145388 United States
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis for L-isoaspartyl-containing protein recognition by the PCMTD1 cullin-RING E3 ubiquitin ligase.
Authors: Eric Z Pang / Boyu Zhao / Cameron Flowers / Elizabeth Oroudjeva / Jasmine B Winter / Vijaya Pandey / Michael R Sawaya / James Wohlschlegel / Joseph A Loo / Jose A Rodriguez / Steven G Clarke
Abstract: A major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining ...A major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining proteome stability and prolonging organismal survival. While repair through methylation by PCMT1 has been previously shown to suppress L-isoaspartyl accumulation, we provide an additional mechanism for L-isoaspartyl maintenance through PCMTD1, a cullin-RING ligase (CRL). We combined cryo-EM, native mass spectrometry, and biochemical assays to provide insight on how the assembly and architecture of PCMTD1 in the context of a CRL complex fulfils this alternative mechanism. We show that the PCMTD1 CRL complex specifically binds L-isoaspartyl residues when bound to AdoMet. This work provides evidence for a growing class of E3 ubiquitin ligases that recognize spontaneous covalent modifications as potential substrates for ubiquitylation and subsequent proteasomal degradation.
ETOC BLURB: Limiting the accrual of L-isoaspartyl damaged proteins is essential during aging. While this is thought to be mediated solely by the repair activity of the protein, PCMT1, Pang al. now ...ETOC BLURB: Limiting the accrual of L-isoaspartyl damaged proteins is essential during aging. While this is thought to be mediated solely by the repair activity of the protein, PCMT1, Pang al. now demonstrate that a related protein, PCMTD1, functions as a cullin-RING ligase to selectively target L-isoaspartyl-damaged substrates for potential regulation by the ubiquitylation-proteosomal system.
HIGHLIGHTS: Atomic cryo-EM structure of CRL5-PCMTD1 determinedArchitecture of PCMTD1 when complexed as a CRL supports ubiquitylation activityPCMTD1 recognizes L-isoaspartyl residues as a recruitment ...HIGHLIGHTS: Atomic cryo-EM structure of CRL5-PCMTD1 determinedArchitecture of PCMTD1 when complexed as a CRL supports ubiquitylation activityPCMTD1 recognizes L-isoaspartyl residues as a recruitment motif for potential CRL activityRecognition of L-isoaspartyl residues is dependent on cofactor engagement.
History
DepositionMay 13, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70612.png

Downloads & links

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Map

FileDownload / File: emd_70612.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened 3D map of N8-CRL5-PCMTD1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 480 pix.
= 356.64 Å		0.74 Å/pix.
x 480 pix.
= 356.64 Å		0.74 Å/pix.
x 480 pix.
= 356.64 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165
Minimum - Maximum-0.033801842 - 0.18604892
Average (Standard dev.)0.00023658593 (±0.0044143647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 356.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70612_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70612_half_map_1.map
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Half map: #1

Fileemd_70612_half_map_2.map
Projections & Slices
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Sample components

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Entire : Neddylated complex of PCMTD1, Elongins B and C, Cullin-5, and RIN...

EntireName: Neddylated complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (N8-CRL5-PCMTD1)
Components
  • Complex: Neddylated complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (N8-CRL5-PCMTD1)
    • Protein or peptide: Protein-L-isoaspartate O-methyltransferase domain-containing protein 1
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C

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Supramolecule #1: Neddylated complex of PCMTD1, Elongins B and C, Cullin-5, and RIN...

SupramoleculeName: Neddylated complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (N8-CRL5-PCMTD1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein-L-isoaspartate O-methyltransferase domain-containing protein 1

MacromoleculeName: Protein-L-isoaspartate O-methyltransferase domain-containing protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.814348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMGGAVSAGE DNDDLIDNLK EAQYIRTERV EQAFRAIDRG DYYLEGYRDN AYKDLAWKHG NIHLSAPCIY SEVMEALKLQ PGLSFLNLG SGTGYLSTMV GLILGPFGIN HGIELHSDVV EYAKEKLESF IKNSDSFDKF EFCEPAFVVG NCLQIASDSH Q YDRIYCGA ...String:
SMGGAVSAGE DNDDLIDNLK EAQYIRTERV EQAFRAIDRG DYYLEGYRDN AYKDLAWKHG NIHLSAPCIY SEVMEALKLQ PGLSFLNLG SGTGYLSTMV GLILGPFGIN HGIELHSDVV EYAKEKLESF IKNSDSFDKF EFCEPAFVVG NCLQIASDSH Q YDRIYCGA GVQKDHENYM KILLKVGGIL VMPIEDQLTQ IMRTGQNTWE SKNILAVSFA PLVQPSKNDN GKPDSVGLPP CA VRNLQDL ARIYIRRTLR NFINDEMQAK GIPQRAPPKR KRKRVKQRIN TYVFVGNQLI PQPLDSEEDE KMEEDIKEEE EKD HNEAMK PEEPPQNLLR EKIMKLPLPE SLKAYLTYFR DK

UniProtKB: Protein-L-isoaspartate O-methyltransferase domain-containing protein 1

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Macromolecule #2: Cullin-5

MacromoleculeName: Cullin-5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.43668 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GEFMATSNLL KNKGSLQFED KWDFMRPIVL KLLRQESVTK QQWFDLFSDV HAVCLWDDKG PAKIHQALKE DILEFIKQAQ ARVLSHQDD TALLKAYIVE WRKFFTQCDI LPKPFCQLEI TLMGKQGSNK KSNVEDSIVR KLMLDTWNES IFSNIKNRLQ D SAMKLVHA ...String:
GEFMATSNLL KNKGSLQFED KWDFMRPIVL KLLRQESVTK QQWFDLFSDV HAVCLWDDKG PAKIHQALKE DILEFIKQAQ ARVLSHQDD TALLKAYIVE WRKFFTQCDI LPKPFCQLEI TLMGKQGSNK KSNVEDSIVR KLMLDTWNES IFSNIKNRLQ D SAMKLVHA ERLGEAFDSQ LVIGVRESYV NLCSNPEDKL QIYRDNFEKA YLDSTERFYR TQAPSYLQQN GVQNYMKYAD AK LKEEEKR ALRYLETRRE CNSVEALMEC CVNALVTSFK ETILAECQGM IKRNETEKLH LMFSLMDKVP NGIEPMLKDL EEH IISAGL ADMVAAAETI TTDSEKYVEQ LLTLFNRFSK LVKEAFQDDP RFLTARDKAY KAVVNDATIF KLELPLKQKG VGLK TQPES KCPELLANYC DMLLRKTPLS KKLTSEEIEA KLKEVLLVLK YVQNKDVFMR YHKAHLTRRL ILDISADSEI EENMV EWLR EVGMPADYVN KLARMFQDIK VSEDLNQAFK EMHKNNKLAL PADSVNIKIL NAGAWSRSSE KVFVSLPTEL EDLIPE VEE FYKKNHYGRK LHWHHLMSNG IITFKNEVGQ YDLEVTTFQL AVLFAWNQRP REKISFENVK LATELPDAEL RRTLWSL VA FPKLKRQVLL YEPQVNSPKD FTEGTLFSVN QEFSLIKNAK VQKRGKINLI GRLQLTTERM REEENEGIVQ LRILRTQE A IIQIMKMRKK ISNAQLQTEL VEILKNMFLP QKKMIKEQIE WLIEHKYILR DESDINTFIY MA

UniProtKB: Cullin-5

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Macromolecule #3: RING-box protein 2

MacromoleculeName: RING-box protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.7215 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVEDGEEP CVLSSHSGSA GSKSGGDKMF SLKKWNAVAM WSWDVECDTC AICRVQVMDA CLRCQAENKQ EDCVVVWGEC NHSFHNCCM SLWVKQNNRC PLCQQDWVVQ RIGK

UniProtKB: RING-box protein 2

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Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #5: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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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

Concentration2.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMHEPES
150.0 mMsodium chloride
1.0 mMDTT
GridModel: SPT Labtech self-wicking R1.2/0.8 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: SPT LABTECH CHAMELEON
DetailsSample was monodisperse and freshly neddylated then gel-filtrated prior to sample vitrification

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 15192 / Average exposure time: 2.64 sec. / 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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1731846
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / Details: Ab initio model generated in cryoSPARC
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 9.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 7521
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Avg.num./class: 11833 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9oma


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: Initial model consisted of the complete complex for PDB entry 9OMA
DetailsEnergy minimized against 3D map of N8-CRL5-PCMTD1 with model of CRL5-PCMTD1 (PDB: 9OMA) then refined in Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9omf:
Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1)

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