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- EMDB-61162: Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer c... -

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Basic information

Entry
Database: EMDB / ID: EMD-61162
TitleCryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer complexed with FNIP1 degron
Map data
Sample
  • Complex: Neddylated Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with FNIP1 degron
    • Protein or peptide: Cullin-2
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Folliculin interacting protein 1
  • Ligand: ZINC ION
KeywordsComplex / E3 ubiquitin ligase / Cullin / Oligomer / LIGASE
Function / homology
Function and homology information


negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / target-directed miRNA degradation / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / elongin complex ...negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / target-directed miRNA degradation / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / elongin complex / Cul7-RING ubiquitin ligase complex / VCB complex / death receptor binding / regulation of cell cycle process / regulation of extrinsic apoptotic signaling pathway via death domain receptors / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / NEDD8 ligase activity / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / positive regulation of cilium assembly / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / regulation of TOR signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / SCF ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cytokinesis / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / nucleotide-excision repair complex / detection of maltose stimulus / regulation of cell cycle phase transition / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / maltose transport complex / Cul4A-RING E3 ubiquitin ligase complex / carbohydrate transport / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / Cul4B-RING E3 ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / regulation of cellular response to stress / limb development / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein monoubiquitination / carbohydrate transmembrane transporter activity / cullin family protein binding / maltose binding / maltose transport / maltodextrin transmembrane transport / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / centrosome duplication / regulation of DNA-templated DNA replication initiation / Formation of HIV elongation complex in the absence of HIV Tat / cilium assembly / RNA Polymerase II Transcription Elongation / ubiquitin-like ligase-substrate adaptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Formation of RNA Pol II elongation complex / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / ubiquitin ligase complex / protein K63-linked ubiquitination / RNA Polymerase II Pre-transcription Events / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / protein K48-linked ubiquitination / transcription-coupled nucleotide-excision repair / post-translational protein modification / positive regulation of TORC1 signaling / regulation of embryonic development / ATP-binding cassette (ABC) transporter complex / replication fork processing / cellular response to amino acid stimulus / transcription corepressor binding / regulation of mitotic cell cycle / negative regulation of canonical NF-kappaB signal transduction / rescue of stalled cytosolic ribosome / site of DNA damage / negative regulation of canonical Wnt signaling pathway / Regulation of BACH1 activity / T cell activation / negative regulation of smoothened signaling pathway
Similarity search - Function
Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminal domain / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile. / Zinc finger, RING-H2-type ...Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminal domain / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Elongin-C / : / Elongin B / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / 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 / Ankyrin repeat / SKP1/BTB/POZ domain superfamily / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing 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
Similarity search - Domain/homology
Folliculin interacting protein 1 / Maltose/maltodextrin-binding periplasmic protein / E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B / Protein fem-1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsDai Z / Liang L / Yin YX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81621063, 31800626 China
CitationJournal: To Be Published
Title: Neddylation induces an intermediate auto-inhibited CRL2FEM1B E3 ubiquitin ligase
Authors: Dai Z / Liang L / Yin YX
History
DepositionAug 14, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61162.png

Downloads & links

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Map

FileDownload / File: emd_61162.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.82526654 - 1.5143561
Average (Standard dev.)-0.00028307515 (±0.020755153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61162_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #1

Fileemd_61162_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Neddylated Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with ...

EntireName: Neddylated Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with FNIP1 degron
Components
  • Complex: Neddylated Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with FNIP1 degron
    • Protein or peptide: Cullin-2
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: Protein fem-1 homolog B
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Folliculin interacting protein 1
  • Ligand: ZINC ION

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Supramolecule #1: Neddylated Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with ...

SupramoleculeName: Neddylated Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with FNIP1 degron
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.92782 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK ...String:
MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK NDRGGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLTETGEY YKQEASNLLQ ESNCSQYMEK VL GRLKDEE IRCRKYLHPS SYTKVIHECQ QRMVADHLQF LHAECHNIIR QEKKNDMANM YVLLRAVSTG LPHMIQELQN HIH DEGLRA TSNLTQENMP TLFVESVLEV HGKFVQLINT VLNGDQHFMS ALDKALTSVV NYREPKSVCK APELLAKYCD NLLK KSAKG MTENEVEDRL TSFITVFKYI DDKDVFQKFY ARMLAKRLIH GLSMSMDSEE AMINKLKQAC GYEFTSKLHR MYTDM SVSA DLNNKFNNFI KNQDTVIDLG ISFQIYVLQA GAWPLTQAPS STFAIPQELE KSVQMFELFY SQHFSGRKLT WLHYLC TGE VKMNYLGKPY VAMVTTYQMA VLLAFNNSET VSYKELQDST QMNEKELTKT IKSLLDVKMI NHDSEKEDID AESSFSL NM NFSSKRTKFK ITTSMQKDTP QEMEQTRSAV DEDRKMYLQA AIVRIMKARK VLRHNALIQE VISQSRARFN PSISMIKK C IEVLIDKQYI ERSQASADEY SYVAHHHHHH

UniProtKB: Cullin-2

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Macromolecule #2: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.045694 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAMYVKLISS DGHEFIVKRE HALTSGTIKA MLSGPGQFAE NETNEVNFRE IPSHVLSKVC MYFTYKVRYT NSSTEIPEFP IAPEIALEL LMAANFLDC

UniProtKB: Elongin-C

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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: 11.748406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMK

UniProtKB: Elongin-B

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Macromolecule #5: Protein fem-1 homolog B

MacromoleculeName: Protein fem-1 homolog B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.412117 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMEGLAGYVY KAASEGKVLT LAALLLNRSE SDIRYLLGYV SQQGGQRSTP LIIAARNGHA KVVRLLLEHY RVQTQQTGTV RFDGYVIDG ATALWCAAGA GHFEVVKLLV SHGANVNHTT VTNSTPLRAA CFDGRLDIVK YLVENNANIS IANKYDNTCL M IAAYKGHT ...String:
GMEGLAGYVY KAASEGKVLT LAALLLNRSE SDIRYLLGYV SQQGGQRSTP LIIAARNGHA KVVRLLLEHY RVQTQQTGTV RFDGYVIDG ATALWCAAGA GHFEVVKLLV SHGANVNHTT VTNSTPLRAA CFDGRLDIVK YLVENNANIS IANKYDNTCL M IAAYKGHT DVVRYLLEQR ADPNAKAHCG ATALHFAAEA GHIDIVKELI KWRAAIVVNG HGMTPLKVAA ESCKADVVEL LL SHADCDR RSRIEALELL GASFANDREN YDIIKTYHYL YLAMLERFQD GDNILEKEVL PPIHAYGNRT ECRNPQELES IRQ DRDALH MEGLIVRERI LGADNIDVSH PIIYRGAVYA DNMEFEQCIK LWLHALHLRQ KGNRNTHKDL LRFAQVFSQM IHLN ETVKA PDIECVLRCS VLEIEQSMNR VKNISDADVH NAMDNYECNL YTFLYLVCIS TKTQCSEEDQ CKINKQIYNL IHLDP RTRE GFTLLHLAVN SNTPVDDFHT NDVCSFPNAL VTKLLLDCGA EVNAVDNEGN SALHIIVQYN RPISDFLTLH SIIISL VEA GAHTDMTNKQ NKTPLDKSTT GVSEILLKTQ MKMSLKCLAA RAVRANDINY QDQIPRTLEE FVGFH

UniProtKB: Protein fem-1 homolog B

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Macromolecule #6: Maltose/maltodextrin-binding periplasmic protein,Folliculin inter...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Folliculin interacting protein 1
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.985301 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYAQ SGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA KGKSALMFNL Q EPYFTWPL ...String:
MGHHHHHHKI 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 EALKDAQTDY DIPTTENLYF QGNKSSLLFK ESEE IRTPN CNCKYCSHPL LGQNVENISQ QEREDIQNSS KELLGISDEC QMISPSDCQE ENAVDVKQYR DK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Folliculin interacting protein 1

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: Quantifoil R0.6/1 / Material: GOLD / Support film - Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 48.69 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 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: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 110858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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