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- EMDB-43572: Human Cullin-1 in complex with CAND2 -

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Basic information

Entry
Database: EMDB / ID: EMD-43572
TitleHuman Cullin-1 in complex with CAND2
Map data
Sample
  • Complex: CAND2-CUL1
    • Protein or peptide: Cullin-1
    • Protein or peptide: Cullin-associated NEDD8-dissociated protein 2
KeywordsComplex / LIGASE
Function / homology
Function and homology information


SCF complex assembly / Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / protein K48-linked ubiquitination ...SCF complex assembly / Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / TBP-class protein binding / intrinsic apoptotic signaling pathway / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / animal organ morphogenesis / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Iron uptake and transport / Negative regulation of NOTCH4 signaling / 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 / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / HEAT-like repeat / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin ...TATA-binding protein interacting (TIP20) / Cullin-associated NEDD8-dissociated protein 1/2 / TATA-binding protein interacting (TIP20) / HEAT-like repeat / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / 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. / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cullin-associated NEDD8-dissociated protein 2 / Cullin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsKenny S / Liu X / Das C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138016 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Human CAND2 in complex with Cullin-1
Authors: Kenny S / Das C / Liu X
History
DepositionJan 31, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43572.png

Downloads & links

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Map

FileDownload / File: emd_43572.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-4.6326394 - 7.570691
Average (Standard dev.)0.008118684 (±0.17707719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43572_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_43572_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 : CAND2-CUL1

EntireName: CAND2-CUL1
Components
  • Complex: CAND2-CUL1
    • Protein or peptide: Cullin-1
    • Protein or peptide: Cullin-associated NEDD8-dissociated protein 2

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Supramolecule #1: CAND2-CUL1

SupramoleculeName: CAND2-CUL1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.294484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SKQIGLDQIW DDLRAGIQQV YTRQSMAKSR YMELYTHVYN YCTSVHQFVG LELYKRLKEF LKNYLTNLLK DGEDLMDESV LKFYTQQWE DYRFSSKVLN GICAYLNRHW VRRECDEGRK GIYEIYSLAL VTWRDCLFRP LNKQVTNAVL KLIEKERNGE T INTRLISG ...String:
SKQIGLDQIW DDLRAGIQQV YTRQSMAKSR YMELYTHVYN YCTSVHQFVG LELYKRLKEF LKNYLTNLLK DGEDLMDESV LKFYTQQWE DYRFSSKVLN GICAYLNRHW VRRECDEGRK GIYEIYSLAL VTWRDCLFRP LNKQVTNAVL KLIEKERNGE T INTRLISG VVQSYVELGL NEDDAFAKGP TLTVYKESFE SQFLADTERF YTRESTEFLQ QNPVTEYMKK AEARLLEEQR RV QVYLHES TQDELARKCE QVLIEKHLEI FHTEFQNLLD ADKNEDLGRM YNLVSRIQDG LGELKKLLET HIHNQGLAAI EKC GEAALN DPKMYVQTVL DVHKKYNALV MSAFNNDAGF VAALDKACGR FINNNAVTKM AQSSSKSPEL LARYCDSLLK KSSK NPEEA ELEDTLNQVM VVFKYIEDKD VFQKFYAKML AKRLVHQNSA SDDAEASMIS KLKQACGFEY TSKLQRMFQD IGVSK DLNE QFKKHLTNSE PLDLDFSIQV LSSGSWPFQQ SCTFALPSEL ERSYQRFTAF YASRHSGRKL TWLYQLSKGE LVTNCF KNR YTLQASTFQM AILLQYNTED AYTVQQLTDS TQIKMDILAQ VLQILLKSKL LVLEDENANV DEVELKPDTL IKLYLGY KN KKLRVNINVP MKTEQKQEQE TTHKNIEEDR KLLIQAAIVR IMKMRKVLKH QQLLGEVLTQ LSSRFKPRVP VIKKCIDI L IEKEYLERVD GEKDTYSYLA

UniProtKB: Cullin-1

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Macromolecule #2: Cullin-associated NEDD8-dissociated protein 2

MacromoleculeName: Cullin-associated NEDD8-dissociated protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.6695 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SAGWSHPQFE KMSTAAFHIS SLLEKMTSSD KDFRFMATSD LMSELQKDSI QLDEDSERKV VKMLLRLLED KNGEVQNLAV KCLGPLVVK VKEYQVETIV DTLCTNMRSD KEQLRDIAGI GLKTVLSELP PAATGSGLAT NVCRKITGQL TSAIAQQEDV A VQLEALDI ...String:
SAGWSHPQFE KMSTAAFHIS SLLEKMTSSD KDFRFMATSD LMSELQKDSI QLDEDSERKV VKMLLRLLED KNGEVQNLAV KCLGPLVVK VKEYQVETIV DTLCTNMRSD KEQLRDIAGI GLKTVLSELP PAATGSGLAT NVCRKITGQL TSAIAQQEDV A VQLEALDI LSDMLSRLGV PLGAFHASLL HCLLPQLSSP RLAVRKRAVG ALGHLAAACS TDLFVELADH LLDRLPGPRV PT SPTAIRT LIQCLGSVGR QAGHRLGAHL DRLVPLVEDF CNLDDDELRE SCLQAFEAFL RKCPKEMGPH VPNVTSLCLQ YIK HDPNYN YDSDEDEEQM ETEDSEFSEQ ESEDEYSDDD DMSWKVRRAA AKCIAALISS RPDLLPDFHC TLAPVLIRRF KERE ENVKA DVFTAYIVLL RQTQPPKGWL EAMEEPTQTG SNLHMLRGQV PLVVKALQRQ LKDRSVRARQ GCFSLLTELA GVLPG SLAE HMPVLVSGII FSLADRSSSS TIRMDALAFL QGLLGTEPAE AFHPHLPILL PPVMACVADS FYKIAAEALV VLQELV RAL WPLHRPRMLD PEPYVGEMSA VTLARLRATD LDQEVKERAI SCMGHLVGHL GDRLGDDLEP TLLLLLDRLR NEITRLP AI KALTLVAVSP LQLDLQPILA EALHILASFL RKNQRALRLA TLAALDALAQ SQGLSLPPSA VQAVLAELPA LVNESDMH V AQLAVDFLAT VTQAQPASLV EVSGPVLSEL LRLLRSPLLP AGVLAAAEGF LQALVGTRPP CVDYAKLISL LTAPVYEQA VDGGPGLHKQ VFHSLARCVA ALSAACPQEA ASTASRLVCD ARSPHSSTGV KVLAFLSLAE VGQVAGPGHQ RELKAVLLEA LGSPSEDVR AAASYALGRV GAGSLPDFLP FLLEQIEAEP RRQYLLLHSL REALGAAQPD SLKPYAEDIW ALLFQRCEGA E EGTRGVVA ECIGKLVLVN PSFLLPRLRK QLAAGRPHTR STVITAVKFL ISDQPHPIDP LLKSFIGEFM ESLQDPDLNV RR ATLAFFN SAVHNKPSLV RDLLDDILPL LYQETKIRRD LIREVEMGPF KHTVDDGLDV RKAAFECMYS LLESCLGQLD ICE FLNHVE DGLKDHYDIR MLTFIMVARL ATLCPAPVLQ RVDRLIEPLR ATCTAKVKAG SVKQEFEKQD ELKRSAMRAV AALL TIPEV GKSPIMADFS SQIRSNPELA ALFESIQKDS ASAPSTDSME LS

UniProtKB: Cullin-associated NEDD8-dissociated protein 2

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5333 / Average exposure time: 4.56 sec. / Average electron dose: 1.28 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4562541
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold model of CAND2 and Cul1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 187280
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.2.0)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-Correlation Coefficient
Output model

PDB-8vvy:
Human Cullin-1 in complex with CAND2

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